Question: how to use DEXSeq with raw exon count matrix downloaded from TCGA
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gravatar for ren.yingxue
20 months ago by
ren.yingxue0 wrote:

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 • 918 views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 20 months ago by ren.yingxue0

Why don't you use dexseq_count.py then ?

ADD REPLYlink written 20 months ago by geek_y9.4k

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.

ADD REPLYlink written 20 months ago by ren.yingxue0

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by geek_y9.4k

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

ADD REPLYlink written 19 months ago by swamyvinny20
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