Hi, I want to use DEXSeq to identify differential exon usage between ~800 cancer vs 90 normal samples from TCGA. I have a matrix of raw exon counts downloaded from TCGA in the format below:
Exon TCGA-66-2742-01A TCGA-L4-A4E5-01A TCGA-86-8671-01A TCGA-77-8008-01A chr1:11874-12227:+ 2 7 15 1 chr1:12595-12721:+ 1 1 3 0 chr1:12613-12721:+ 1 1 3 0
The problem is that DEXSeq requires to use dexseq_count.py to perform exon counts for each sample using bam/sam as input, and then combine these files into an object "countFiles", which will then be used in the DEXSeq function "DEXSeqDataSetFromHTSeq". Since I only have a matrix of raw exon counts and don't have individual BAM/SAM, I wonder how I can still use DEXSeq. Any suggestions are appreciated! Thank you!