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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Independent Filtering in R #114

Closed sanatbhadsavle closed 2 years ago

sanatbhadsavle commented 2 years ago

Hi, Is there any particular reason why the DEseq2 pipeline in TEtranscripts has the independent filtering option turned to 'FALSE'? Is this just a preference?

olivertam commented 2 years ago

Hi,

I think this might be a holdover from when we first worked with DESeq2 (where we were trying not to use independent filtering to mimic DESeq). However, I agree that independent filtering is more appropriate when using DESeq2. I will update this.

Thanks.

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