How featureCounts define the gene length
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niuyw ▴ 20
@niuyw-11650
Last seen 3.0 years ago
Beijing, China

Hi, I'm using featureCounts from the Rsubread package. But I have a question about the gene length returned by featrureCounts.
I've read the case study here: http://bioinf.wehi.edu.au/RNAseqCaseStudy/, and the combination of featureCounts and edgeR is wonderful.
We often need to get the R/FPKM values from a RNAseq experiment, and I just used the rpkm() function in edgeR. This function takes the gene length as input, which I got by featureCounts. So I wonder how featureCOunts define the gene length? This will affect the result. I've tried google but got little information.

Any help will be appreciated,thank you very much!

featurecounts rnaseq rsubread • 2.4k views
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@gordon-smyth
Last seen 3 hours ago
WEHI, Melbourne, Australia

It is the total number of DNA bases that belong to any exon for that gene.

If you type ?featureCounts to get help on featureCounts, then read the description of the output value, it says:

"For each meta-feature, the Length column gives the total length of genomic regions covered by features included in that meta-feature. Note that this length will be less than the sum of lengths of features included in the meta-feature when there are features overlapping with each other."

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Thanks! According the doc of featureCounts, it's the total number of intersection of exons that belong to the gene, not the total number of DNA bases that belong to any exon for that gene.

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I have to disagree with you -- the featureCounts documentation does not make any reference to an "intersection of exons". As far I can remember, gene length has always been correctly described in the featureCounts documentation and agrees with my answer. The quote I give from the documentation demonstrates this.

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