diff --git a/README.md b/README.md index f83b3d1..6efaafa 100644 --- a/README.md +++ b/README.md @@ -81,6 +81,7 @@ Dependencies - R (>=3.6.1) - Python (>=3.6.0) +- Perl ### Software packages required diff --git a/scripts/split_bam2clusters.sh b/scripts/split_bam2clusters.sh index 3dc45f3..579db2c 100755 --- a/scripts/split_bam2clusters.sh +++ b/scripts/split_bam2clusters.sh @@ -33,17 +33,17 @@ do ${SAMTOOLS_PATH}/samtools index -@ $ncore $file0 ${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \ --bam $file0 --binSize 100 --skipNonCoveredRegions \ - --outFileName $fname_bw & + --outFileName $fname_bw fname_bedgraph=${file0/.bam/.bedgraph} - ${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \ - --outFileFormat bedgraph --bam $file0 --binSize 100 --skipNonCoveredRegions \ - --outFileName $fname_bedgraph & - wait + #${DEEPTOOLS_PATH}/bamCoverage --numberOfProcessors max --normalizeUsing BPM \ + # --outFileFormat bedgraph --bam $file0 --binSize 100 --skipNonCoveredRegions \ + # --outFileName $fname_bedgraph + #wait done ## move signal to output/signal mv ${output_dir}/*bw ${OUTPUT_DIR}/signal/ -mv ${output_dir}/*bedgraph ${OUTPUT_DIR}/signal/ +#mv ${output_dir}/*bedgraph ${OUTPUT_DIR}/signal/ echo "The bam file was split into different clusters!"