I have a question regarding the input data into DExSeq. I'm working with level 3 TCGA exon_quantification data which looks likes this:
Hybridization REF TCGA-3C-AAAU-01A-11R-A41B-07 TCGA-3C-AALI-01A-11R-A41B-07 TCGA-3C-AALJ-01A-31R-A41B-07
exon raw_counts raw_counts raw_counts raw_counts
chr1:11874-12227:+ 29 23 18 2
chr1:12595-12721:+ 7 10 1 0
chr1:12613-12721:+ 7 10 1 0
chr1:12646-12697:+ 6 5 1 0
I have the raw counts for each exon. The problem I'm having is turning this into something I can use in DexSeq. I don't have access to any of the orginal SAM/BAM files, and my dataset just has raw counts which I think I can use in DexSeq but the problem I'm having is converting the exon co-ordinates into transcript IDs. I have a gtf file downloaded. I was wondering is anyone has any suggestions on how to do this or perhaps any bioconductor tools that will give me that output I need.
Thanks in advance.