minor change

wbaopaul · Feb 16, 2021 · 2b4f438 · 2b4f438
1 parent f753bbc
commit 2b4f438
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -81,6 +81,7 @@ Dependencies
 
 -   R (&gt;=3.6.1)
 -   Python (&gt;=3.6.0)
+-   Perl
 
 ### Software packages required
 

diff --git 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!"
-Original file line number
+Diff line change
@@ Expand Up / @@ -81,6 +81,7 @@ Dependencies @@
     -   R (&gt;=3.6.1)
     -   Python (&gt;=3.6.0)
+    -   Perl
     ### Software packages required
@@ Expand Down @@