Hi guys, I'm a newbie in the RNA Seq world. I'm analyzing some RNA seq data (HiSeq) and doing this, I'm following the best practice guideline available online form different sources. Briefly I performed the alignment to the reference genome, the merge, I removed duplicates, then I performed the sorting, indexing and finally using bedtools multicov I ended up having the reads count per RefSeq. My point is that I would like to have a gene level expression measure but after the counts I have reads counts per transcript variants. in other words I have multiple transcripts per gene with corresponding reads count but I would like to have one reads counts per gene. How do you deal with this issue?
Thanks in advance