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Question: RNA STAR to DESeq2
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gravatar for nikelle.petrillo
3 months ago by
nikelle.petrillo0 wrote:

Hi all, 

I aligned my PE reads using STAR and I used the GeneCounts option to get a count matrix. I would like to use this count matrix with DESeq2, however, I'm having trouble formatting STAR's gene count into a count matrix that is recognized and works with DESeq2. Does anyone have any tips/ideas how I should be importing/formating this matrix into DESeq2?

Thanks, 

Nikelle 

ADD COMMENTlink modified 3 months ago by James W. MacDonald45k • written 3 months ago by nikelle.petrillo0

You can also have a look at featureCounts (http://bioinf.wehi.edu.au/featureCounts/). It needs a gtf as annotation input, the bam files. You can run it in pe or se. It's pretty nice and produces a table with samples as columns and genes as rows.

ADD REPLYlink written 3 months ago by mat.lesche20
1
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald45k wrote:

DESeq2 has a pretty comprehensive vignette that you could peruse, which includes an example of what the count matrix should look like. I would take a look there first. Also, unless you tell us what you have tried, and what your counts matrix looks like, it's very difficult to give any advice.

ADD COMMENTlink written 3 months ago by James W. MacDonald45k
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