wwood
Calculating RPKM of metaT reads against a collection of MAGs
Hi, I've been trying for months now to use coverM to map metaT reads against a collection of MAGs. My goal is to output the RPKM for each MAG. But even though coverM runs with no error, it tells me that no read mapped. Which makes no sens because I got BAM files with another tool and they are very interesting in terms of content and number of reads mapping to the reference.
I wonder if min covered fraction is removing them? I think the default 10% isn't good for metaT and I'd use 0.
Ok, can I try that and come back to you ? In any cases thanks for your advice !
I have these kind of RPKM in output thanks to your suggestion, does it look like something normal or is it total garbage to your opinion ? (I never used RPKM before so I have no idea of what it should look like)
I wonder if min covered fraction is removing them? I think the default 10% isn't good for metaT and I'd use 0.
Could you tell me why you'd use 0 ? I fear that it could produce false positives, am I right to think that ?
Hi,
It might have false positives, but you are also doing something I've not seen before - using transcriptome coverage to rule in or out genomes. Typically RPKM is on a per-gene basis, not a per-genome. Since it is quite non-standard, I wouldn't want to have any strong opinions without looking at the data.