Does software significantly impact fold change values?

Question

[margarett]

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?

Answer 1

[Jeremy Leipzig]

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