Picrust2 - fragment-insertion error


(Lena Lapidot) #21

Got it, thank you for the explanation.

Is it ok that I used deblured rep-seqs and feature table?


(Gavin Douglas) #22

PICRUSt2 is agnostic to the OTU picking or denoising pipeline used, so yes deblur is fine.

Gavin


(Lena Lapidot) #23

Great, everything worked! Thank you.

Now I have a question regarding the output files.
There is a table of KO’s and a table of pathway abundances.
According to what are the pathways classified?
Is there a way to classify the KO tables according to KEGG levels?


(Gavin Douglas) #24
  • The pathways are classified as MetaCyc pathways. You can see descriptions of all MetaCyc pathway ids in the file “picrust2/default_files/description_mapfiles/metacyc_pathways_info_prokaryotes.txt.gz” (in the PICRUSt2 github repo).

  • KEGG is now closed source which is why PICRUSt2 only supports MetaCyc pathways. If you want to use KEGG pathways then you’ll need to specify a custom mapfile as input to this standalone script: https://github.com/picrust/picrust2/wiki/Infer-pathway-abundances. Note that swapping in different mapfiles is not yet supported with the qiime2 plugin.

Best,

Gavin


(Lena Lapidot) #25

Awesome, I managed to do the KEGG analysis. Thank you for the explanation.

One more question.
Is it possible to do minpath analysis with qiime2?


(Gavin Douglas) #26

The MinPath analysis mapping EC numbers to MetaCyc pathways is run by default. Currently you can’t use custom mapping files (such as KEGG) with the qiime2 plugin.

Gavin


(Lena Lapidot) #27

100%, I understand.
Thank you!