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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
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RNA-seq: Tuxedo pipeline deprecated #2288

Open mshukla1 opened 5 years ago

mshukla1 commented 5 years ago

This was reported by one of the users during Seattle Workshop.

Data analyzed with Cufflinks in particular were reported to be susceptible to batch effects. The tuxedo pipeline was replaced in 2016 with https://www.nature.com/articles/nprot.2016.095 according to https://www.biostars.org/p/327842/

We need to update the algorithms used in the RNA-seq service to make sure it uses the latest and widely accepted tools.

aswarren commented 5 years ago

Note, it is not the whole tuxedo pipeline. Back in 2016 we did replace Cufflinks with Stringtie. Stringtie crashed a lot. So we reverted. It is still wrapped in the prok tuxedo code so we can try it again now. Also note we would still likely use cuffdiff instead of ballgown. @chmao1 can comment further.

mshukla1 commented 4 years ago

So, this is a non-issue and we can close the ticket?