I did some googling about mRNAseq pipeline and built that pipeline. So I would like to know if my pipeline is okay.
Reference genome : Human gencode GRCh37
Aligner : STAR
Expression quantification : RSEM
Gene count table convert? : tximport
Statistical test : DESeq2
it seems like people use htseq or featureCount for gene count table and put it into edgeR or DESeq2. I am not sure, if I go for RSEM to run DESeq2 instead of htseq or featureCount. I tried kallisto and slueth, but I want to stick to this traditional alignment method.
Any advice would be apprieciated.