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,