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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Add DeSeq2 support https://forum.ugene.net/forum/YaBB.pl?num=1565083701 Message started by Mike Shelk on Aug 6^th, 2019 at 4:28pm

Title: Add DeSeq2 support
Post by Mike Shelk on Aug 6^th, 2019 at 4:28pm

Hi!

Currently UGENE uses cuffdiff for differential expression analysis. Cuffdiff is outdated and produces more false positives than many other tools. I think many people will be glad if you add a more modern tool for the differential expression analysis, for example DeSeq2. A comparison can be found in the paper "How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?" (2016).

Title: Re: Add DeSeq2 support
Post by Olga Golosova on Aug 12^th, 2019 at 1:41pm

Hi Mike!

Thank you for the feedback!

We plan to integrate DeSeq2, however for now we can't specify the exact deadlines when this will be done.