Michael Hoggard

icon indicating a website link https://scholar.google.co.nz/citations?hl=en&user=B6fMVfUAAAAJ

icon company @GenomicsAotearoa icon location Auckland, New Zealand icon location Data science | Bioinformatics and genomics | Environmental science and ecology.

Results 8 comments of Michael Hoggard

Trained models for RNA viruses

Hi @YiJessePi , Apologies for the slow reply, but no, in the end I simply decided to omit DeepVirFinder from my RNA virus workflow. And in the case of RNA...

Problem during prepare the database

Just chiming in here as well to see if there had been any updates/progress on this? We've been having the same issue for a while now. We've had previous installs...

Problem during prepare the database

Thanks for the reply. Our run finally looks like it has worked now. It required 12 days and max ~400 GB RAM. But our final database directory is 799 GB,...

Problem during prepare the database

Hi @saras224, Congrats on getting it up and running. I haven't spent that much time with the distill output yet, but I'm guessing the figures generated are meant as a...

Update coverage normalisation script(s)

Note: also check R dependencies for this. `dynamic_require()` doesn't seem to be correctly installing some libraries. This might be due to needing to manually select the CRAN location.

Update coverage normalisation script(s)

@DininduSenanayake . Ah, good point. "dplyr" , "tibble" , "readr", "tidyr", "fuzzyjoin", "stringr", "matrixStats", "edgeR", "EDAseq" edgeR and EDAseq are installed via BiocManager, so that's also required for that step....

Update coverage normalisation script(s)

@DininduSenanayake Ah brilliant! That's great to know thanks.

Update viral processing steps to VirSorter2 and DRAM-v

@DininduSenanayake Yeah, to confirm, *not* using `VIBRANT` this year (we still use it in our own research though) so you can leave it as is! And will instead incorporate `VirSorter/2.2.3-gimkl-2020a-Python-3.8.2...