RNA-seq with normalized cpm count
1
0
Entering edit mode
8 months ago
GiV17 ▴ 50

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 • 340 views
ADD COMMENT
0
Entering edit mode
8 months ago
bk11 ★ 3.0k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1745 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6