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Question: How featureCounts define the gene length
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gravatar for niuyw
13 months ago by
niuyw0
Beijing, China
niuyw0 wrote:

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!

ADD COMMENTlink modified 13 months ago by Gordon Smyth32k • written 13 months ago by niuyw0
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gravatar for Gordon Smyth
13 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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."

ADD COMMENTlink modified 13 months ago • written 13 months ago by Gordon Smyth32k

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.

ADD REPLYlink modified 13 months ago • written 13 months ago by niuyw0
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