Question

RNA STAR to DESeq2

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nikelle.petrillo • 0

@nikellepetrillo-13687

Last seen 7.4 years ago

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

deseq2 count matrix star • 8.5k views

ADD COMMENT • link updated 7.4 years ago by James W. MacDonald 67k • written 7.4 years ago by nikelle.petrillo • 0

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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 REPLY • link 7.4 years ago mat.lesche ▴ 110

score 1 · Answer 1 · 2017-08-08

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

United States

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 COMMENT • link 7.4 years ago James W. MacDonald 67k