Unable to find Levels in pathways

[Aditya Bhardwaj]

Hello, 

I used Picrust2 for predicting some functional gene as described in the tutorial( I used "Full pipeline script"). How can I get level L1, l2 and L3 of the pathway?

Also, I am getting EC numbers but I want full names. Is this possible in picrust2?

Thank you

Aditya

[Gavin Douglas]

Hi there,

I used Picrust2 for predicting some functional gene as described in the tutorial( I used "Full pipeline script"). How can I get level L1, l2 and L3 of the pathway?

The default pathways are different than in PICRUSt1, but you can get the old format by following the instructions here: https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions#how-can-i-run-categorize_by_functionpy-like-in-picrust1

Also, I am getting EC numbers but I want full names. Is this possible in picrust2?

Yes - you can see how to add a column with function descriptions in this section of the tutorial: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.4.1)#add-functional-descriptions

Cheers,

Gavin

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/fbc340c6-0b67-44eb-a1e4-1bf679c251e8n%40googlegroups.com.

[Aditya Bhardwaj]

Thank you for your response. I was able to get descriptions in all my outputs. But, I am still struggling with 
levels in pathways. Can you please tell me which package should I install in R for this analysis? Is there any tutorial for this?

Thank you,

Aditya

[Gavin Douglas]

You just need base R, but to get the legacy pathway format isn’t a PICRUSt2 command it’s just the rough R code that I show as an example (which you would need to run yourself manually). We don’t support the old KEGG pathways level output in PICRUSt2, sorry!

Gavin

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/3c1202af-336e-4eb6-8088-0e0734612480n%40googlegroups.com.