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Commit 820b69ac authored by Holger Brandl's avatar Holger Brandl
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cont. cs analysis

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dge_workflow/dge_utils.sh
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...@@ -188,7 +188,7 @@ bamLabels=$(echo "$bamFiles" |sed 's!.*/!!' | sed 's/_ca.bam//g' | sed 's/.bam// ...@@ -188,7 +188,7 @@ bamLabels=$(echo "$bamFiles" |sed 's!.*/!!' | sed 's/_ca.bam//g' | sed 's/.bam//
## see how well bam files correlate using untrimmed data ## see how well bam files correlate using untrimmed data
bcCmd="bamCorrelate bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels --plotFile='bc.pdf' --outFileCorMatrix='bc.txt' --numberOfProcessors=6 --corMethod spearman --zMin 0.5 --zMax 1" bcCmd="bamCorrelate bins --bamfiles $(echo $bamFiles | xargs echo) --labels $bamLabels --plotFile='bc.pdf' --outFileCorMatrix='bc.txt' --numberOfProcessors=6 --corMethod spearman --zMin 0.5 --zMax 1"
mysub "${project}__bamcorrelate" "$bcCmd" -q long -n 4 -R span[hosts=1] | blockScript mysub "${project}__bamcorrelate" "$bcCmd" -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
mailme "$project: bamcorrelate done in $(pwd)" mailme "$project: bamcorrelate done in $(pwd)"
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