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dib-lab / eel-pond

mRNAseq assembly, evaluation, and expression analysis
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0-install-aws.rst salmon installation #44

Open taylorreiter opened 7 years ago

taylorreiter commented 7 years ago

I am under the impression that the gather-counts.py script for salmon file processing works with salmon 0.8.0, and is non-functional for salmon 0.7.2, however I might be wrong.

johnsolk commented 7 years ago

Thank you - yes, gather-counts.py seems to be dependent on salmon version. You indicated this didn't work so we need to update.

My understanding is @ctb wrote this script for these workshops: 2016 workshop and 2015 workshop with old version of salmon. We tested this script with version 0.7 and worked fine, but now the version is updated again >0.8 so script probably needs to be modified for new version.

In the meantime, we put this script together during NGS 2016 which will put all .quant into one .csv table:

https://raw.githubusercontent.com/ljcohen/ngs2016_important_files/master/merge_counts.py