Hi community!!! I have profiled shotgun metagenome data with MetaPhlAn. Now, I want to do statistical analysis (e.g. alpha-, beta- diversity comparison, rarefaction graph, boxplots, PCOA, etc) with the output data. Can anyone please suggest me which software can I use? (provided, I don’t know language like R, python, etc.)
Thanks and regards, DC7
Thanks sir. It can import MetaPhlAn output. But I'm getting error like this:
Any idea?
Hi,
Not sure. From the error it seems related with the fact that for that particular taxonomic annotation you got something annotated at genus level -
g__Gemella
-, but not annotated at family levelf__Bacillales_unclassified
, that is a higher rank just above the genus. This is quite strange, because if you know what is the genus, you should know the family.I think the program is complaining about that. I guess this is related with the taxonomic database that you've used. Was this database the database recommend by MetaPhlAn? If so I suggest you to contact the developers of MetaPhlAn to try to address this issue.
António
Yes sir. The database is CHOCOPHLAN v30 which is recommended by MetPhlAn3. I have created a thread regarding this problem in the metaphlan forum as well as in biostars. Thanks