Commit 437126b7 authored by Jeremy Mathews's avatar Jeremy Mathews
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PR Checklist

parent c9b7cbad
Pipeline #4390 passed with stages
in 888 minutes and 31 seconds
......@@ -116,6 +116,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
plotProfile | plotProfile.png | Plot profile of the TSS region
plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
## Common Quality Control Metrics
+ These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
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......@@ -90,6 +90,8 @@ diffPeaks | normcount_peaksets.txt | Use only for replicated samples; peak set v
diffPeaks | pca.pdf | Use only for replicated samples; PCA of peak location and peak intensity
diffPeaks | *_diffbind.bed | Use only for replicated samples; bed file of peak locations between replicates
diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks between replicates
plotProfile | plotProfile.png | Plot profile of the TSS region
plotProfile | computeMatrix.gz | Compute Matrix from deeptools to create custom plots other than plotProfile
## Common Quality Control Metrics
+ These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
......
#!/bin/bash
#plotProfile.sh
bws=`ls *.bw`
gtf=`ls *.gtf *.bed`
bws=$(ls *.bw)
gtf=$(ls *.gtf *.bed)
computeMatrix reference-point \
--referencePoint TSS \
......
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