This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Convert mothur classify.seqs output to BIOM format

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

metagenomics mothur r phyloseq
• 4,330 views • link
updated by h.mon h.mon • written by pkozyrev • pkozyrev

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)

• 0 views • link
written by badribio badribio

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

• 0 views • link
written by pkozyrev • pkozyrev

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

Thank you for your help anyway!

• 0 views • link
written by pkozyrev • pkozyrev

1 answer

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

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

• 0 views • link
written by h.mon h.mon

Thank you!

I've already understood.

• 0 views • link
written by pkozyrev • pkozyrev

Log in to answer this question.

More posts like this