diff --git a/README.md b/README.md index e2361654d9dda12c7692d8bd1f8e8edd95f0fda4..a5bcdeb373cd19ccafb4d8248c61a1af2a815599 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 18ae6ed89ce26535ecd5b055013b94c693706866..193f3ec3a395fce2253c3b90e9e7e9de8a7359c2 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 3ab4d901ee4a3c9da7cc1aa55c8215f831805f02..7f62dc5bdd9e13026315222b076b8b939f839d00 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 \