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?