Output directory missing: macs2/consensus/deseq2

[ktrns]

Hi again,

I am going through Documentation/results_description.html to understand which output I have. I do not find bwa/mergedLibrary/macs2/consensus/deseq2. Instead, I find bwa/mergedLibrary/macs/consensus and qc, i.e. no macs2 and no further deseq2 subdirectories. Can you comment on that? Were you still running macs2, but no deseq2?

Many thanks in advance!
Katrin

[drpatelh]

Hi @ktrns ! You will only find the deseq2 directory if you have both multiple experimental groups (e.g. treatment and control) and biological replicates in your design file. Can you send me design.csv here please?

[ktrns]

Hi @drpatelh, Thanks for your quick reply! We only have one replicate per group, so that would explain it. But the folder is still called 'macs' rather than 'macs2', as it is mentioned in the results_description.html.

[drpatelh]

Yep. It should be macs and not macs2 in the documentation 👍

This discrepancy also exists in the nf-core/chipseq documentation which will need to be corrected too.
https://github.com/nf-core/chipseq/blob/master/docs/output.md

[ktrns]

@drpatelh, great, thanks for letting me know. I will soon run the chipseq pipeline too, so good to know.

[drpatelh]

Fixed in #49