I have a sequenced data of 75 bp PE for control samples and 150 bp PE for treatment samples. I am using HISAT2 for mapping and alignment. I got a gene count matrix after using Stringtie. I am wondering if I could use the gene count matrix directly for DESEQ2 for the differential gene expression analysis or if I need to convert the counts to RPKM.
Does anyone have any suggestion? I would highly appreciate it.