Open mhyleung opened 4 years ago
Hi Marc,
That shouldn't be a problem, though just be aware that you'll either need to:
Use FishTaco's built-in inference method for estimating the genomic content of your taxa from the associated functional profiles
Create your own custom table of genomic content for your taxa.
Hopefully that helps!
Best, Alex
Hi Alex Thanks for the quick response. It seems that the more sensible way to do this will be to adopted option number 2, as the kraken2 database would have some non-overlapping taxa not covered by the FishTaco built-in inference method.
In this case, are you aware of any scripts out there that would allow me to, from a list of downloaded genomes, perform functional annotation and KO identification (probably involving tools such as prodigal/prokka and eggnog) as well as counting the copy number of the KOs for each genome?
Thanks so much!
Regards Marcus
Hi Marcus,
I have not performed much whole genome functional annotation, so there may be better tools out there that I am not aware of, but I think you may be able to use one of the web-based annotation tools KEGG offers. These would be BlastKoala/GhostKoala (https://www.kegg.jp/ghostkoala/, https://www.sciencedirect.com/science/article/pii/S002228361500649X?via%3Dihub) or the newer KofamKoala (https://www.genome.jp/tools/kofamkoala/, https://academic.oup.com/bioinformatics/article/36/7/2251/5631907). I do not have much experience with these tools, but I think they might be what you're looking for.
Best, Alex
Thanks Alex. I will give it a try and update my progress here in case I got it to work.
Regards
Marcus
Hi @mhyleung, did you get succeeded in making genomic_content for your taxa (for Non-metaphlan2 taxonomy)? if yes, please can you share your experience? I am also in the situation now, Thanks, Khem
Hi Khem
I ended up not working on this as this part of analysis was no longer needed for my current work. I shall update this when I get around this! Good luck!
Marcus
Dear all
I have been trying to compare the use of MetaPhlan2 and other classification tools (e.g. kraken2 and others). Will feeding a taxonomic and functional output fils generated by kraken2 and HUMAnN2 be problematic for FishTaco?
Thanks
Marc