Matteo Bonfanti
Matteo Bonfanti
Hi @nick-phillips and @jeremymsimon, I have recently been involved in the development of the pipeline, and I have experienced the same problem that you are describing. I think that there...
closed by #252
This has now been fixed by #441, I am closing the issue!
Hi, I do not know if this is the case, but I had a similar issue lately. My problem was that after trimming I was left with sequences that were...
yep, sure... When you start from fastq files, you have to provide a sample sheet that contains sample labels and condition labels. With the contrast file you specify the condition...
I just want to be sure I’m following your reasoning: is the concern mainly about the pipeline being runnable in non-standard cases without a samplesheet, or about the possible inconsistency...
I see your point, and I agree. In that sense, my preference would be to simplify the pipeline by removing the condition column altogether, so that the contrast file always...
Hi @afombravo, Just as a side note, I think that the command "count" of mageck can be run directly on count matrices, and the compute only summary statistics and normalize...
Hi @LeonHornich, I solved the issue in #247 by skipping the "unstable" files in the snapshot. When we merge the code from that PR you can update your branch from...
@LeonHornich I did the merge from dev myself, because there was conflict in the snaphot to solve... finger crossed :-)