ismapper
Tags: insertion-sequences transposons comparative-genomics bactopia-tool
Identificar posições de sequências de inserção em genomas bacterianos.
Esta Ferramenta Bactopia usa o ISMapper para identificar sítios de inserção de transposases em genomas bacterianos a partir de dados de sequenciamento de reads curtos.
Uso
Bactopia CLI:
bactopia --wf ismapper \
--bactopia /path/to/your/bactopia/results
Nextflow:
nextflow run bactopia/bactopia/workflows/bactopia-tools/ismapper/main.nf \
--bactopia /path/to/your/bactopia/results
Saídas
Arquivos de Saída Esperados
<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│ └── tools
│ └── ismapper-<TIMESTAMP>
│ └── is1016.fasta
│ ├── logs
│ │ ├── <SAMPLE_NAME>.log
│ │ ├── nf.command.{begin,err,log,out,run,sh,trace}
│ │ └── versions.yml
│ └── supplemental
│ └── IS1016V1_IS1595_IS1016
│ ├── <SAMPLE_NAME>_IS1016V1_IS1595_IS1016_left_final.fastq.gz
│ ├── <SAMPLE_NAME>_IS1016V1_IS1595_IS1016_right_final.fastq.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_10_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_11_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_12_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_13_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_14_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_15_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_16_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_17_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_18_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_19_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_1_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_20_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_21_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_22_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_23_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_24_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_25_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_26_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_27_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_28_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_29_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_2_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_30_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_31_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_32_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_33_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_34_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_35_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_36_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_37_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_38_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_39_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_3_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_40_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_41_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_42_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_43_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_44_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_45_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_46_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_47_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_48_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_49_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_4_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_50_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_51_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_52_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_53_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_54_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_55_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_56_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_57_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_58_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_59_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_5_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_60_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_61_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_62_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_63_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_64_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_65_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_66_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_67_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_68_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_69_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_6_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_70_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_71_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_72_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_73_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_74_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_74_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_74_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_75_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_75_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_75_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_76_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_76_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_76_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_77_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_77_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_77_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_78_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_78_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_78_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_79_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_7_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_80_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_80_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_80_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_8_table.txt
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_closest.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_intersect.bed.gz
│ ├── <SAMPLE_NAME>__<SAMPLE_NAME>_9_table.txt
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_10_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_11_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_12_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_13_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_14_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_15_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_16_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_17.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_17.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_17_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_17_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_17_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_18.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_18.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_18_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_18_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_18_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_19.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_19.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_19_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_19_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_19_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_1_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_2.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_2.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_20.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_20.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_20_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_20_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_20_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_21.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_21.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_21_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_21_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_21_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_22.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_22.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_22_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_22_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_22_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_23.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_23.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_23_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_23_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_23_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_24.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_24.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_24_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_24_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_24_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_25.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_25.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_25_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_25_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_25_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_26.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_26.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_26_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_26_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_26_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_27.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_27.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_27_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_27_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_27_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_28.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_28.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_28_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_28_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_28_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_29.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_29.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_29_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_29_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_29_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_2_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_2_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_2_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_3.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_3.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_30.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_30.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_30_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_30_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_30_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_31.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_31.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_31_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_31_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_31_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_32.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_32.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_32_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_32_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_32_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_33.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_33.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_33_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_33_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_33_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_34.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_34.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_34_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_34_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_34_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_35.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_35.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_35_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_35_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_35_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_36.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_36.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_36_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_36_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_36_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_37.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_37.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_37_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_37_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_37_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_38.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_38.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_38_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_38_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_38_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_39.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_39.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_39_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_39_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_39_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_3_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_3_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_3_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_4.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_4.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_40.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_40.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_40_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_40_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_40_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_41.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_41.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_41_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_41_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_41_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_42.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_42.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_42_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_42_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_42_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_43.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_43.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_43_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_43_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_43_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_44.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_44.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_44_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_44_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_44_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_45.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_45.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_45_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_45_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_45_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_46.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_46.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_46_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_46_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_46_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_47.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_47.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_47_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_47_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_47_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_48.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_48.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_48_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_48_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_48_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_49.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_49.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_49_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_49_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_49_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_4_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_4_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_4_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_5.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_5.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_50.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_50.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_50_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_50_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_50_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_51.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_51.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_51_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_51_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_51_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_52.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_52.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_52_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_52_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_52_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_53.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_53.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_53_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_53_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_53_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_54.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_54.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_54_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_54_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_54_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_55.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_55.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_55_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_55_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_55_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_56.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_56.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_56_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_56_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_56_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_57.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_57.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_57_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_57_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_57_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_58.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_58.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_58_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_58_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_58_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_59.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_59.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_59_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_59_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_59_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_5_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_5_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_5_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_6.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_6.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_60.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_60.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_60_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_60_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_60_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_61.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_61.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_61_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_61_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_61_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_62.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_62.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_62_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_62_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_62_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_63.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_63.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_63_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_63_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_63_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_64.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_64.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_64_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_64_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_64_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_65.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_65.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_65_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_65_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_65_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_66.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_66.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_66_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_66_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_66_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_67.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_67.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_67_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_67_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_67_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_68.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_68.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_68_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_68_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_68_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_69.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_69.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_69_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_69_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_69_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_6_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_6_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_6_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_7.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_7.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_70.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_70.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_70_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_70_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_70_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_71.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_71.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_71_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_71_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_71_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_72.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_72.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_72_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_72_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_72_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_73.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_73.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_73_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_73_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_73_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_74.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_74.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_74_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_74_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_74_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_75.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_75.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_75_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_75_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_75_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_76.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_76.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_76_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_76_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_76_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_77.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_77.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_77_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_77_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_77_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_78.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_78.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_78_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_78_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_78_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_79.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_79.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_79_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_79_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_79_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_7_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_7_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_7_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_8.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_8.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_80_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_80_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_80_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_8_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_8_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_8_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_9.sorted.bam
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_9.sorted.bam.bai
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_9_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_9_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_left_<SAMPLE_NAME>_9_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_1.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_1.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_10.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_10.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_10_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_10_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_10_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_11.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_11.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_11_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_11_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_11_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_12.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_12.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_12_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_12_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_12_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_13.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_13.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_13_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_13_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_13_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_14.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_14.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_14_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_14_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_14_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_15.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_15.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_15_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_15_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_15_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_16.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_16.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_16_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_16_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_16_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_17.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_17.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_17_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_17_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_17_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_18.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_18.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_18_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_18_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_18_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_19.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_19.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_19_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_19_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_19_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_1_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_1_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_1_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_2.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_2.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_20.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_20.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_20_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_20_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_20_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_21.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_21.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_21_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_21_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_21_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_22.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_22.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_22_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_22_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_22_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_23.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_23.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_23_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_23_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_23_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_24.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_24.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_24_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_24_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_24_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_25.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_25.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_25_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_25_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_25_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_26.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_26.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_26_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_26_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_26_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_27.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_27.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_27_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_27_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_27_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_28.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_28.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_28_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_28_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_28_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_29.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_29.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_29_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_29_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_29_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_2_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_2_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_2_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_30.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_30.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_30_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_30_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_30_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_31.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_31.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_31_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_31_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_31_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_32.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_32.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_32_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_32_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_32_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_33.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_33.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_33_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_33_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_33_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_34.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_34.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_34_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_34_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_34_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_35.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_35.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_35_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_35_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_35_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_36.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_36.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_36_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_36_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_36_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_37_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_38_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_39_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_3_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_40_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_41_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_42_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_43_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_44_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_45_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_46_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_47_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_48_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_49_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_4_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_50_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_51_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_52_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_53_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_54_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_55_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_56_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_57_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_58_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_59_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_5_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_60_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_61_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_62_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_63_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_64_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_65_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_66_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_67_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_68_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_69_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_6_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_70_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_71_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_72_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_73_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_74_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_75_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_76_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_77_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_78_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_79_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_7_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_80_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_merged.sorted.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_8_unpaired.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9.sorted.bam
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9.sorted.bam.bai
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_finalcov.bed.gz
│ ├── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_merged.sorted.bed.gz
│ └── <SAMPLE_NAME>_right_<SAMPLE_NAME>_9_unpaired.bed.gz
└── bactopia-runs
└── ismapper-<TIMESTAMP>
└── nf-reports
├── ismapper-dag.dot
├── ismapper-report.html
└── ismapper-timeline.html
Resultados por Amostra
| Arquivo | Descrição |
|---|---|
*.vcf | Arquivo VCF com as chamadas de sítios de inserção |
*.txt | Resumo dos resultados de sítios de inserção |
Resultados Consolidados
| Arquivo | Descrição |
|---|---|
ismapper.tsv | Arquivo TSV consolidado com os resultados do ISMapper de todas as amostras |
Trilha de Auditoria
A seguir estão os arquivos que podem ajudar a entender quais parâmetros e versões de programas foram utilizados.
Logs
Cada processo executado terá uma pasta chamada logs. Nessa pasta há arquivos úteis para consulta, caso necessário.
| Extensão | Descrição |
|---|---|
| .begin | Arquivo vazio usado para indicar que o processo foi iniciado |
| .err | Contém as saídas STDERR do processo |
| .log | Contém as saídas STDERR e STDOUT do processo |
| .out | Contém as saídas STDOUT do processo |
| .run | O script que o Nextflow usa para preparar/limpar arquivos e enfileirar processos com base no perfil definido |
| .sh | O script executado pelo bash para o processo |
| .trace | O relatório de rastreamento do Nextflow para o processo |
| versions.yml | Arquivo no formato YAML com as versões dos programas |
Relatórios do Nextflow
Esses relatórios do Nextflow fornecem um ótimo resumo da sua execução. Eles podem ser usados para otimizar o uso de recursos e estimar custos esperados em plataformas de nuvem.
| Nome do arquivo | Descrição |
|---|---|
| ismapper-dag.dot | A visualização DAG do Nextflow |
| ismapper-report.html | O Relatório de Execução do Nextflow |
| ismapper-timeline.html | O Relatório de Linha do Tempo do Nextflow |
| ismapper-trace.txt | O relatório de Rastreamento do Nextflow |
Parâmetros
Parâmetros Obrigatórios
Define onde o pipeline deve encontrar os dados de entrada e salvar os dados de saída.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--bactopia | string | O caminho para os resultados do Bactopia a serem usados como entradas |
Parâmetros do ISMapper
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--reference | string | Genoma de referência para tipagem no formato GenBank | |
--insertions | string | Arquivo multifasta com a(s) sequência(s) de inserção a serem mapeadas | |
--ismapper_min_clip | integer | 10 | Tamanho mínimo para a região softclipped ser extraída do mapeamento inicial |
--ismapper_max_clip | integer | 30 | Tamanho máximo para as regiões softclipped serem incluídas |
--ismapper_cutoff | integer | 6 | Profundidade mínima para a região mapeada ser mantida no arquivo bed |
--ismapper_novel_gap_size | integer | 15 | Distância em pares de bases entre os flancos esquerdo e direito para ser considerado um novo hit |
--ismapper_min_range | number | 0.9 | Percentual mínimo do tamanho do gap para ser considerado um hit conhecido |
--ismapper_max_range | number | 1.1 | Percentual máximo do tamanho do gap para ser considerado um hit conhecido |
--ismapper_merging | integer | 100 | Valor para a fusão dos hits esquerdos e direitos nos arquivos bed, simplificando o cálculo das regiões mais próximas e interseccionadas |
--ismapper_all | boolean | false | Ativa o relatório de todos os alinhamentos para o bwa |
--ismapper_minqual | integer | 30 | Pontuação de qualidade de mapeamento para o bwa |
Parâmetros de Filtragem
Use estes parâmetros para especificar quais amostras incluir ou excluir.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--include | string | Um arquivo de texto contendo nomes de amostras (um por linha) a serem incluídas na análise | |
--exclude | string | Um arquivo de texto contendo nomes de amostras (um por linha) a serem excluídas da análise |
Parâmetros Opcionais
Estes parâmetros opcionais podem ser úteis em determinadas situações.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--outdir | string | bactopia | Diretório base para gravar os resultados |
--skip_compression | boolean | false | Os arquivos de saída não serão comprimidos |
--datasets | string | O caminho para armazenar em cache os datasets | |
--keep_all_files | boolean | false | Mantém todos os arquivos de análise criados |
Parâmetros de Limite Máximo de Recursos
Define o limite máximo de recursos solicitados para qualquer job individual.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--max_retry | integer | 3 | Número máximo de tentativas de um processo antes de permitir que ele falhe. |
--max_cpus | integer | 4 | Número máximo de CPUs que podem ser solicitadas para qualquer job individual. |
--max_memory | string | 128.GB | Quantidade máxima de memória que pode ser solicitada para qualquer job individual. |
--max_time | string | 240.h | Quantidade máxima de tempo que pode ser solicitada para qualquer job individual. |
--max_downloads | integer | 3 | Número máximo de amostras para baixar simultaneamente |
Parâmetros de Configuração do Nextflow
Parâmetros para ajustar a configuração do Nextflow.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--nfconfig | string | Um arquivo de configuração compatível com Nextflow para perfis personalizados, carregado por último e que substituirá variáveis existentes se definido. | |
--publish_dir_mode | string | copy | Método usado para salvar os resultados do pipeline no diretório de saída. (opções: symlink, rellink, link, copy, copyNoFollow, move) |
--infodir | string | ${params.outdir}/pipeline_info | Diretório para manter os logs e relatórios do Nextflow do pipeline. |
--force | boolean | false | O Nextflow sobrescreverá arquivos de saída existentes. |
--cleanup_workdir | boolean | false | Após a execução bem-sucedida do Bactopia, o diretório work será excluído. |
Opções de configuração institucional
Parâmetros usados para descrever perfis de configuração centralizados. Estes não devem ser editados.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--custom_config_version | string | master | ID do commit Git para configurações institucionais. |
--custom_config_base | string | https://raw.githubusercontent.com/nf-core/configs/master | Diretório base para configurações institucionais. |
--config_profile_name | string | Nome do perfil de configuração institucional. | |
--config_profile_description | string | Descrição do perfil de configuração institucional. | |
--config_profile_contact | string | Informações de contato do perfil de configuração institucional. | |
--config_profile_url | string | Link de URL do perfil de configuração institucional. |
Parâmetros de Perfil do Nextflow
Parâmetros para ajustar a configuração do Nextflow.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--condadir | string | Diretório que o Nextflow deve usar para os ambientes Conda | |
--registry | string | quay.io | Registro de onde baixar os containers Docker. |
--datasets_cache | string | <HOME>/.bactopia/datasets | Diretório onde os datasets baixados devem ser armazenados. |
--singularity_cache | string | Diretório onde as imagens Singularity remotas são armazenadas. | |
--singularity_pull_docker_container | boolean | Em vez de baixar diretamente as imagens Singularity, força o fluxo de trabalho a baixar e converter containers Docker. | |
--force_rebuild | boolean | false | Força a sobrescrita de ambientes pré-construídos existentes. |
--queue | string | general,high-memory | Nome(s) da(s) fila(s) separados por vírgula a serem usados por um agendador de jobs (ex.: AWS Batch ou SLURM) |
--cluster_opts | string | Opções adicionais para passar ao executor. (ex.: SLURM: '--account=my_acct_name' | |
--container_opts | string | Opções adicionais para passar ao Apptainer, Docker ou Singularity. (ex.: Singularity: '-D pwd' | |
--disable_scratch | boolean | false | Todos os arquivos intermediários criados nos nós de trabalho serão transferidos para o nó principal. |
Parâmetros Úteis
Parâmetros pouco utilizados que podem ser convenientes em alguns casos.
| Parâmetro | Tipo | Padrão | Descrição |
|---|---|---|---|
--monochrome_logs | boolean | Não usar saídas de log coloridas. | |
--nfdir | boolean | Exibe o diretório para o qual o Nextflow baixou o Bactopia | |
--sleep_time | integer | 5 | O tempo (em segundos) que o Nextflow aguardará após configurar os datasets antes da execução. |
--validate_params | boolean | true | Define se os parâmetros devem ser validados em relação ao esquema em tempo de execução |
--help | boolean | Exibe o texto de ajuda. | |
--wf | string | bactopia | Especifica qual fluxo de trabalho ou Ferramenta Bactopia executar |
--list_wfs | boolean | Lista os fluxos de trabalho e Ferramentas Bactopia disponíveis para uso com '--wf' | |
--show_hidden_params | boolean | Mostra todos os parâmetros ao usar --help | |
--help_all | boolean | Um alias para --help --show_hidden_params | |
--version | boolean | Exibe o texto da versão. |
Composição
Este fluxo de trabalho utiliza os seguintes subworkflows:
- ismapper - Identificar sítios de inserção de transposases em genomas bacterianos.
Citações
Se você usar este fluxo de trabalho em sua análise, por favor cite os seguintes trabalhos.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
ISMapper
Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16, 667 (2015)