Hi all,

I would like to know, if there is a possibility to assign differential exons to specific transcripts.

I have run DEXSeq on my data set and have found (e.g.) one gene of interest with differential exon usage. This gene though has several transcripts (58 according to DEXSeq, biologically speaking still 14 different transcripts. s below).

I would like to know, if it is possible to assign a specific transcript to the differentiated exon(s), so that i can claim one transcript is higher expressed than another. After reading the DEXSeq information and also searching the internet, I assume it is not possible to do in DEXSeq. Therefore I would like to know, if there is a different way of getting this information.

I have also ran cuffQuant-cuffDiff on the bam files and have the count files. Is it a valid option to use the fold-change results from the cuffDiff run together with the DEXSeq results to claim such transcripts to be differentially expressed?

is there a different way of doing it?

thanks

Assa

RSEM, salmon, kallisto, cufflinks, and likely many other aligners are all intended to map reads to transcripts. Salmon and kallisto are much faster than the other two. Then you need to use something like EBseq to incorporate the uncertainty of your transcript counts into the comparisons. You could also use sleuth, which will take as input either kallisto data directly (or if you use Rob Patro's fork, salmon data).