I'm analysing RNA seq data from the ENCODE CSHL long RNA seq to see differential expression between two genes sharing a chromosomal locus. I am really not familiar with bio-informatics at all, a wet bench researcher through & through. Somehow, I managed to get on with a linux platform and started with a single sample to analyse with cufflinks, and further aligned it to the reference genome using IGV. What I see is that the transcripts from cufflinks for the two genes are on the same strand in IGV, as opposed to the reality wherein they are in different strands, going away from each other. I'm pretty convinced that its a technical mistake, pertaining to the fact that I'm not suave with these informatic analyses. But if anybody could please point out how it is done properly or what could possibly have gone wrong, I would be really grateful.
Many thanks, Vaish