Comparison of samples of different read lengths in differential gene expression analysis

Question

[rthapa]

Hi,

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.

Thanks

Answer 1

[swbarnes2]

Do not convert; raw integer gene counts is just what DESeq wants. It will do the library normalization that it wants itself.