Is your feature request related to a problem? Please describe
For microbiome/metagenomic screening analysis, typically the main file type is an OTU table. We already have this with Kraken, but do not generate such as thing for MALT based alignments.
Describe the solution you'd like
I've discovered there are utility tools in the the MEGAN6 than can get us almost there quite easily from an RMA6 file - it can extract for (one sample at a time) all taxa/functional category, and counts for each.
The two options are:
compute-comparison
rma2info
With the latter also in principle allowing filtering to different domains, but also to different taxonoimc rank.
Would have to write a little script to combine each sample, and perform filtering, but this cna be done very easily e.g. with R.
Describe alternatives you've considered
Nix
Additional context
Would likely have to be added with DSL2, as the bioconda MEGAN package requires JDK >=11.
jfy133
commented
6 months ago
Is your feature request related to a problem? Please describe
For microbiome/metagenomic screening analysis, typically the main file type is an OTU table. We already have this with Kraken, but do not generate such as thing for MALT based alignments.
Describe the solution you'd like
I've discovered there are utility tools in the the MEGAN6 than can get us almost there quite easily from an RMA6 file - it can extract for (one sample at a time) all taxa/functional category, and counts for each.
The two options are:
With the latter also in principle allowing filtering to different domains, but also to different taxonoimc rank.
Would have to write a little script to combine each sample, and perform filtering, but this cna be done very easily e.g. with R.
Describe alternatives you've considered
Nix
Additional context
Would likely have to be added with DSL2, as the bioconda MEGAN package requires JDK >=11.