Question

RSEM to CPM?

0

Entering edit mode

4.5 years ago

hq.huang11.6 ▴ 10

Hello,

I download the bulk RNA data from the cbioportal. The count is RSEM. I want to convert RSEM into CPM. Anyone know how to do this!!! Thank you for your help!!!

rna RNA • 1.4k views

ADD COMMENT • link updated 4.5 years ago by ATpoint 89k • written 4.5 years ago by hq.huang11.6 ▴ 10

score 1 · Answer 1 · 2021-03-24

You can read RSEM output into tximport to summarize it to the gene level (tximport) and then feed it to any tool th get normalized counts, e.g. DESeq2 or edgeR:

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#DESeq2

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR