RNA-seq with normalized cpm count

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

rna-seq deseq2 edger

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updated 2.4 years ago by Ram

• written 2.4 years ago by GiV17 •

1 answer

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.

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written 2.4 years ago by bk11 •

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