RNA-seq with normalized cpm count

Question

[GiV17]

Hi all,

I have a question. I have a cpm matrix count of a rnaseq experiment obtained from metatranscriptomics analysis. How can I perform a differentially analysis with deseq2 or edgeR?

Help me.

Thanks

Answer 1

[bk11]

You cannot use CPM count matrix for DE in both DESeq2 and edgeR. These both tools require you to have absolute raw count data. It is recommended to get either raw count or get raw fastq files and obtain count matrix.