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

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

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

rna-seq

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updated 7.5 years ago by swbarnes2

• written 7.5 years ago by rthapa •

1 answer

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

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written 7.5 years ago by swbarnes2

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