From 437126b7cd59bcb47a911c0a92aa454f0a7fa3ea Mon Sep 17 00:00:00 2001 From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu> Date: Thu, 18 Jul 2019 09:54:50 -0500 Subject: [PATCH] PR Checklist --- README.md | 2 ++ docs/index.md | 2 ++ workflow/scripts/plotProfile.sh | 4 ++-- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e236165..a5bcdeb 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/docs/index.md b/docs/index.md index 18ae6ed..193f3ec 100644 --- a/docs/index.md +++ b/docs/index.md @@ -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. diff --git a/workflow/scripts/plotProfile.sh b/workflow/scripts/plotProfile.sh index 3ab4d90..7f62dc5 100644 --- a/workflow/scripts/plotProfile.sh +++ b/workflow/scripts/plotProfile.sh @@ -1,8 +1,8 @@ #!/bin/bash #plotProfile.sh -bws=`ls *.bw` -gtf=`ls *.gtf *.bed` +bws=$(ls *.bw) +gtf=$(ls *.gtf *.bed) computeMatrix reference-point \ --referencePoint TSS \ -- GitLab