Does software significantly impact fold change values?
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5 months ago
margarett • 0

I am using STAR to map reads and then I am using DESeq2 to make differential analysis. Originally this was made with Cufflinks and there were 308 differentially expressed genes - I have 0 because the fold change values are lower than 2. It is possible the software makes such a change or it could be other mistakes?

Cufflinks STAR DESeq2 • 248 views
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Entering edit mode
5 months ago

Yes there is the lfc shrinkage feature of DESeq2 which will reduce your fold changes, especially when you don't have many replicates https://www.biostars.org/post/search/?query=shrinkage+deseq2

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