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how to use DEXSeq with raw exon count matrix downloaded from TCGA

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!

rna-seq exon r dexseq
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updated by Biostar Biostar • written by ren.yingxue • ren.yingxue

Why don't you use dexseq_count.py then ?

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written by GouthamAtla GouthamAtla

thank you for the comments. I cannot use dexseq_count.py because I don't have the BAM files for the ~890 samples. I only have a matrix of raw exon counts downloaded from TCGA.

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written by ren.yingxue • ren.yingxue

To identify differential exon usage, you need to know which is the parent gene name for different exons. If you have that information, you can convert your matrix to the DEXSeq count format.

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written by GouthamAtla GouthamAtla

Did you ever figure out how to do it? I'm trying to do the same thing

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written by swamyvinny • swamyvinny

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