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Old 06-15-2015, 04:26 PM   #1
stormin
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Default HTSeq count to expression level

Hi,

I understand that the raw HTSeq output is number of reads mapped to each gene (correct me if I'm wrong). Is there an easy way of converting counts to gene expression? The method should take into account gene length as well as total seq depth to be comparable between samples.

Also, I use DESeq2 to do differential expression using HTSeq raw output, is that a valid method? Does DESeq2 automatically take into account gene length?

Thank you!
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Old 06-15-2015, 11:14 PM   #2
dpryan
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If you really wanted to, you could convert the counts to RPKM or FPKM, though you shouldn't do statistics on those.

Alternatives to DESeq2 include edgeR and limma/voom, both of which will accept the same counts. DESeq2 doesn't account for gene length because it's constant between group. If you have a gene length bias between samples that's confounding things then look at the CQN package.
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Old 06-16-2015, 09:32 AM   #3
stormin
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Quote:
Originally Posted by dpryan View Post
If you really wanted to, you could convert the counts to RPKM or FPKM, though you shouldn't do statistics on those.
Thanks for the concise answer, are there any scripts that can do this conversion?
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Old 06-16-2015, 09:34 AM   #4
dpryan
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I think edgeR has a function to do that if you supply the gene lengths. That's such a simple thing to compute that I suspect most people just write a script as needed.
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Old 06-16-2015, 10:01 AM   #5
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Sounds good, thanks!
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