Hi,
a collaborator of mine is doing correlation analysis of gene expression using a RNA-seq data from TGCA but our protein of interest (the antiapoptotic Bcl-xL) derived from an alternative splicing event. Since we should distinguish out right isoform from the shortest one (Bcl-xS), which has the opposite cellular function, my collaborator downloaded the RNA-seq data specific for the different isoforms and we found that two different UCSC transcripts (the "main" uc002wwl.3 and uc002wwn.3) encodes for Bcl-xL. My question is related to the correct way to manage these data: should we add the contribution of both UCSC transcript or working with the mean of the two values for each sample? Thanks in advance,
Chiara
i've checked this:
Thanks a lot Pierre, I checked the table you sent and I noticed only a difference in the second exon in which the Start is the same while the End is different for 18nt. In your opinion I should work only with the the first sequence uc002wwl.3 - indicated as the main one - or I should take into account also the second one?