Classification of reads/contigs

Commands in mothur
1

Dear dr. Schloss et al,

I’m working with MiSeq data, and I would like to classify the reads/contigs but I want to maintain the the amount of reads/contigs.

When doing metagenomic sequencing, I would like to see something like
organism1: 500 contigs
organism2: 1000 contigs

I’ve been looking at the MiSeq SOP, but so much is happening there, so if you could point me in the right direction that would be awesome.

Edit, to clarify, I guess what I’m looking for is the sequencing depth/coverage per taxa/OTU/classification. I have no problem with doing some programming to combine this information. But I would need the right output for this :smiley:

Sincerely,

Marley

2

Sorry, I’m confused by what you want to do. Do you want to produce a shared file to know how many sequences come from each OTU per sample? That’s what the SOP takes you to.