I have many meganized files from shotgun sequencing data containing bacteria, but also non-bacterial taxa. I tried to disable non-bacterial groups in the comparison setting as one can do when only working with one sample. Unfortunately, this seems not possible for the comparison setting. Am I missing out on something or do I have to do this per single sample and then compare? Finally, by doing so I want the KEGG results to only represent bacterial functions.
I figured that the funcionality I searched for might not be available. Anyways, I realized that it is possible to run “diamond makedb” like this:
“diamond makedb --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp --in nr.gz --db nr_tax”
By adding this additional information to the db one can later blast against a selection based on NCBI taxon identifiers. --taxonlist 2 limits the blast search to only sequences derived from bacteria.
diamond blastx -p 12 --query 1.fasta --db nr_tax.dmnd --taxonlist 2 --daa 1.daa
After that, one can meganize the daa-files (including KEGG etc.) and import all samples using the comparison function. This way, the KEGG window only shows bacterial functions.
This worked for me!
Thanks, this is useful to know