FPKM

[Biofarmer]

Hi, thanks for your very useful tool, and the version I am working with is 0.6.1. One question about the coverm contig -m rpkm. As mentioned in the the link (https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/), "saying RPKM when you have paired-end reads is just weird, so don’t do it". I have the paired-end reads now, if running with coverm contig -m rpkm, the reported coverage is RPKM or FPKM? Thanks

[wwood]

Hi,

Apologies for the slow response here.

CoverM does not treat paired reads differently to how it treats single-ended reads. So if each read from a pair map to a contig, both will count independently towards the rpkm. So I think the answer to your question is "RPKM".

In future it might be possible to implement FPKM, where only a single count would be applied in the above scenario, but I have no immediate plans to implement that feature - of course pull requests are welcomed.

HTH, ben

[Biofarmer]

Thanks a million for your reply.