I am trying to run DESeq2 using HTseq count as input but I am running in the following error every time, I already checked and input data is correct.
Error in Ops.factor(a$V1, l[]$V1) :
level sets of factors are different
Calls: DESeqDataSetFromHTSeqCount → sapply → sapply → lapply → FUN → Ops.factor
I have SINGLE file per treatment (two treatments) and they have same number of lines (outpu htseq)