Question: Read coverage normalization
0
gravatar for iraia.munoa
10 weeks ago by
iraia.munoa60
iraia.munoa60 wrote:

Hi everybody! I was wondering if there is a need of normalizing read coverage when converting bam results to bedgraph or bigwing for RNA-seq sample visualization. I have used TMM normalization for RNA-seq DEGs analysis and I want to visualize this results in UCSC genome browser. I have been reading about bamCoverage options to normalize read coverage, but I don't know if it is really needed or mandatory when working with RNA-seq data. And if it is recomendable to do that what type of normalization is better? (RPKM, CPM, BPM, TPM) Is it related to use the TMM normalization for DEG and to use some kind of read coverage normalization for visualization?

Any other recomended tool would be also welcome!

Thanks in advance,

Iraia

ADD COMMENTlink written 10 weeks ago by iraia.munoa60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1861 users visited in the last hour