Groups for fastq files

This is a very basic question, but I can’t seem to figure it out. I’m following the Miseq SOP with 16S V4 2X250 reads, no problem, but now I’m trying to do something different with some of the output. I have biological replicates as well as treatment variables that I would like to group together for classify.otu or summary.tax, so that I get output that is merged by different grouping levels for generating taxonomy piechart figures in KronaTools. Basically I need a cons.tax.summary file using my grouping variables. The miseq sop gives me a groups file with sequence names for each fastq file name, but I can’t figure out how to incorporate my own grouping variables into a groups file. I’m sure I’m missing something very obvious.

Pie charts! Surely mothur output deserves a better fate in life than ending up in a piechart :slight_smile:

You might want to try merge.groups

Pat

Thank you! I am just starting to learn to use mothur in ways that is not just following the miseq SOP, I think my problem was a misunderstanding of what a group file is all about, but merge.groups should work. I do want to make all the fancy-pants graphics, but I’m still crawling.

Welcome! Feel free to check out http://www.riffomonas.org/minimalR/ if you’re interested in seeing how to use R to generate plots from mothur output files.

Pat

hahaha you spoke of piecharts in schlossdom and live to tell the tale!

Here’s my starting point for analyzing microbiome datasets in R

LOL, thank you! I am limping along but getting places. To be fair, those krona charts are pretty neat, where you can click through the different taxonomy levels :stuck_out_tongue:

I agree, I like the krona plots too. I make them for people that have me run mothur and encourage them to have the krona plot open while they do their stats