Just a quick question and some advice. I've indexed my target organism's genome and I am now aligning my cleaned reads back to the genome with Star again. My reads were cleaned with Trimmomatic.
I've read that people regularly use cufflinks package for all in one analysis;however, I would be keen on using EdgeR. Once my reads have been aligned. Is there anyway I can use the SAM/ converted BAM files to calculate counts then feed them into R and EdgeR? Most of my experience has so far been in de novo assembly.
Are there any good tutorials I can visit online?