search

borenstein-lab / fishtaco

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts
Other
23 stars 4 forks source link

Using FishTaco based on non-MetaPhlan2 taxonomic info #6

Open mhyleung opened 4 years ago

mhyleung commented 4 years ago

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

engal commented 4 years ago

Hi Marc,

That shouldn't be a problem, though just be aware that you'll either need to:

  1. Use FishTaco's built-in inference method for estimating the genomic content of your taxa from the associated functional profiles

  2. Create your own custom table of genomic content for your taxa.

Hopefully that helps!

Best, Alex

mhyleung commented 4 years ago

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

engal commented 4 years ago

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

mhyleung commented 4 years ago

Thanks Alex. I will give it a try and update my progress here in case I got it to work.

Regards

Marcus

khemlalnirmalkar commented 3 years ago

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

mhyleung commented 3 years ago

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