Question: Convert mothur classify.seqs output to BIOM format
0
gravatar for pkozyrev
2.2 years ago by
pkozyrev10
pkozyrev10 wrote:

I got a lot of problems trying to convert output of mothur classify.seqs to BIOM format so that I can import data into phyloseq R package. I have FASTA file with paired-end reads already being merged with PEAR program.

I aligned my sequences to SILVA database with this command

mothur > align.seqs(fasta=sample.fasta, reference=silva.bacteria.fasta, processors=4, flip=t)

and then I classified it using the same database

mothur > classify.seqs(fasta=sample.align, reference=silva.bacteria.fasta, taxonomy=silva.bacteria.silva.tax, cutoff=80)

After this procedure I got different files: "sample.summary", "sample.silva.wang.taxonomy" and "sample.silva.wang.tax.summary". But I don't know how to import them into phyloseq R package.

I've read here https://github.com/joey711/phyloseq/issues/245 about shared file from which I can create BIOM file, but I don't have .list or .group files for make.shared command.

Can someone help?

Sincerely yours,

Petr

phyloseq mothur metagenomics R • 1.6k views
ADD COMMENTlink modified 2.2 years ago by h.mon26k • written 2.2 years ago by pkozyrev10
2

1) Why would you use pear? when mothur has make.contigs, 2) When you say you have fasta file do you mean you have fastq file? 3) what is the error message you get when you use this command

make.biom(shared=final.tx.1.subsample.1.pick.shared, contaxonomy=final.tx.1.cons.taxonomy)

ADD REPLYlink written 2.2 years ago by badribio240

Thank you for your quick response!

1) Ah, sorry, I didn't mention that I omit some steps in mothur pipeline because I wanted to compare only RDPTools classifier and mothur classifier performance

2) As far as I understood, mothur align.seqs and mothur classify.seqs commands work with fasta files so I converted my fastq file with merged reads to fasta

3) The problem is that I don't have shared file because I don't have .list and .group files to make it

Petr

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by pkozyrev10

crosspost http://seqanswers.com/forums/showthread.php?t=75774

I guess you got your answer, need to make otus..

ADD REPLYlink written 2.2 years ago by badribio240

Yeah, it isn't a good practice. My bad.

Thank you for your help anyway!

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by pkozyrev10
1
gravatar for h.mon
2.2 years ago by
h.mon26k
Brazil
h.mon26k wrote:

To make a .list file, see cluster, cluster.split or phylotype.

To make a .group file, see make.group.

ADD COMMENTlink written 2.2 years ago by h.mon26k

Thank you!

I've already understood.

ADD REPLYlink written 2.2 years ago by pkozyrev10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1555 users visited in the last hour