Normalization of read - Githubissues

dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

https://dieterichlab.org/software/

GNU General Public License v3.0

36 stars 20 forks source link

Normalization of read #86

Closed aashishps closed 2 years ago

aashishps commented 3 years ago

can anyone please tell about is DCC provides normalised reads if not then how to normalise them and how to do differential expression analysis of circRNA.

tjakobi commented 3 years ago

Dear @aashishps,

DCC provides not normalized raw counts of splice junction and linear read counts.

For normalization you might use the edgeR R package which can also be used for differential expression analysis.

Another option would be www.github.com/dieterich-lab/circtest which is able to compare circRNA expression in two (or more) different conditions.

Cheers, Tobias