RNA Seq FAQ: What if the gene was never present/expressed in control sample?
1
0
Entering edit mode
10 months ago
Dr SKY ▴ 20

This is a very simple question and forgive me for sounding dumb in this case What if a gene was never expressed in the control sample? How do you determine the expression value change in treated condition using RNA Seq (if the gene expressed only under treated condition)? Will the gene be considered as novel?

RNA-Seq • 323 views
ADD COMMENT
1
Entering edit mode
10 months ago
ATpoint 55k

Most tools use prior counts to avoid computing infinite fold changes.

You can get more information by starting with these answers from the developers of DESeq2 and edgeR:

For DESeq2: https://support.bioconductor.org/p/64014/

For edgeR: https://support.bioconductor.org/p/57440/

ADD COMMENT
0
Entering edit mode

Thank you for your response.

ADD REPLY

Login before adding your answer.

Traffic: 2373 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