Ben J Woodcroft

icon indicating a website link https://research.qut.edu.au/cmr/team/ben-woodcroft icon indicating an email [email protected]

icon company Queensland University of Technology icon location Brisbane, Australia icon location Assoc. prof. of microbial informatics at the Centre for Microbiome Research (CMR)

Results 187 comments of Ben J Woodcroft

Method ena-ascp failed

Hi, My suspicion is that there is some issue with your ascp install. Has it ever worked? Downloading that run works fine for me: ``` $ kingfisher get -r SRR14018896...

Discussion/request: Read extraction for multiple references

Hi @strejcem thanks for the thought, but I think this functionality is a bit far outside the current structure of CoverM at the moment. Perhaps in the future.

"relative_abundance" option was not provided in "contig" mode

Hi @microjishuai apologies for the slow response here. I can't see any reason why whyat you suggest is a poor idea. You can actually achieve the same thing with a...

Question abount the genome module of coverm

Hi @quliping, Thanks for the kind words. If I understand you correctly, it is (3) which coverm uses.

Filtering by MapQ

Good suggestion Specier. Initial (final?) implementation is at https://github.com/wwood/CoverM/pull/222 if you wanted to take it for a spin.

Filtering by MapQ

Thanks for the enthusiasm Spencer.

Calculating RPKM of metaT reads against a collection of MAGs

I wonder if min covered fraction is removing them? I think the default 10% isn't good for metaT and I'd use 0.

Calculating RPKM of metaT reads against a collection of MAGs

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...

singlem container issue

Hi, Thanks for sorting through this. The sort issue was easy to address, just added the coreutils package to the conda spec. I haven't tested but assume it will be...

Feature Request: support sralite format.

I like this idea, but haven't had the time just yet. WDYT about this being implemented as a `--via-sralite` flag so you can get the fastq file, as well as...