atacseq
atacseq copied to clipboard
nf-core
Mini-issues in the reporting
Hello there,
As usual, I am so glad I can run your pipeline for our clients! :-)
This time around, I found some irregularities in the MultiQC report, and just wanted to list them here for you:
- "MACS2 peak FRiP score": Percentages are always at 100%, so the plot is not very meaningful if you have just 1 number
- "MERGED REP: featureCounts", "MERGED REP: DESeq2 PCA plot", "MERGED REP: DESeq2 sample similarity" are listing results for all samples, not merged replicates
And a mini-typo here: https://github.com/nf-core/atacseq/blob/master/docs/output.md You are missing the "deseq2" in the path:
- bwa/mergedLibrary/macs/<PEAK_TYPE>/consensus/<COMPARISON>/
- bwa/mergedLibrary/macs/<PEAK_TYPE>/consensus/sizeFactors/
Again @drpatelh - the pipelines are really useful, so thanks for your work. Best wishes Katrin
Hi there,
Another one I just noticed: The sample colours in the "FRiP score" plots are flipped, compared to the other plots.
Best wishes and thanks a lot, Katrin
