I have a question regarding input file into DexSeq. I've read the DexSeq manual and see that it requires a SAM/BAM file to generate the counts file. The problem is that I have neither the SAM/BAM file as I have taken RNASeq level 3 data from the TCGA site which contains the chromosome start and end position for each exon along with raw counts for each exon. So I'm guessing I can skip the the first two parts outlined by the DexSeq manual because I already have my raw counts. I also have my gtf file, my question is how can I use my gtf file to get the transcript ids from the chromosome positions in the TCGA dataset so that I can input it into DexSeq, and carry out my analysis. Apologies if this seems like an obvious solution, I'm new to bioinformatics.