How to analyze qiime2 after obtaining picrust2 results

author ： Deaf speech and blind face

to examine ：Listenlii

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This article mainly solves the problem ：

1、QIIME2 finish PICRUSt2 after , Only the output pathway id, How to compare to get pathway description?

2、PICRUSt2 After getting the result , How to analyze ？

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1. pathway ID --- pathway description

PICRUSt2 After result output , Will get based on KEGG And MetaCyc Channel prediction .KEGG yes 2011 Year version , It is suggested not to use .

So the following introduction MetaCyc： Direct use PICRUSt2 If the software is made, it will output directly pathway description, And in the QIIME2 The following methods are needed to do it in .

Read in metacyc Downloaded from the official website pathway id And description documents

Download address ：

https://metacyc.org/group?id=biocyc17-61025-3865826896

id <- read_csv("All-pathways-of-MetaCyc.txt",col_names = T)
dsct <- read_delim("All-pathways-of-MetaCyc-2.txt",col_names = T,delim = "\t") # Pay attention to read_csv There is an error in the number of rows read ！
id_dsct <- cbind(id,dsct = dsct$Pathways)

Save all metacyc Database pathway id And access description

write.table(id_dsct,file = "all_metacyc_id_dsct.tsv",row.names = F,col.names = T,quote = F,sep ="\t")

Import pcirust2 Output result of ：

1、 Export all id, Input to metacyc database ;

2、 hold id Replace with a description , Output STAMP The input file of

pic_output <- read_tsv("feature-table.biom.tsv",col_names = T)
metacyc_input <- pic_output$`OTU-ID`
write.table(metacyc_input,file = "metacyc_input.tsv",row.names = F,col.names = F,quote = F,sep ="\t")

stamp_input <- merge(pic_output,id_dsct,all.x = T,by.x = "OTU-ID",by.y = "Pathways")
write.table(stamp_input,file = "stamp_input.tsv",row.names = F,col.names = F,quote = F,sep ="\t")

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2. PICRUSt2 After getting the result , What more ？

The final output result is also composed data , therefore ... First of all, we know that there is no best statistical model ; secondly , Can we do all kinds of multivariate statistical analysis ？ Whether the differential pathway can STAMP、ANCOM、ALDEx2 Try it all ？

How to explain depends on yourself . You can check the path you are concerned about one by one in combination with the following hierarchical tree .

At the same time, you can also create your own filtered differential path table .

Links are as follows ：https://metacyc.org/smarttables

（ flowers 10s After you sign up , Put the metacyc_input.tsv After import , Can generate mysmarttables, Then you can dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot dot ...

Because I'm just blind , I don't know how to use this completely smarttable, We're not going to teach you how to do it , I think it's OK to refer to the hierarchical tree above . To learn more, see this video tutorial ：

https://biocyc.org/webinar.shtml）

The following figure shows how to import metacyc_input.tsv

Last , Spend most of this week on this , I hope this article can help you on the way to scientific research ;

thank “ Xiao Yu who needs encouragement ” Guidance of .

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