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Question: RNA STAR to DESeq2
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gravatar for nikelle.petrillo
11 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 11 months ago by James W. MacDonald46k • written 11 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 11 months ago by mat.lesche40
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gravatar for James W. MacDonald
11 months ago by
United States
James W. MacDonald46k 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 11 months ago by James W. MacDonald46k
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