Deunique

Commands in mothur
1

Dear Mothur group,

For my data i followed 454 SOP and in that there is unique command to get names files. I wanted to know upto which command data is still unique. Is “cons.tax.summary” is taxonomy with original redundant data or its still unique.
And if I wish to do sequence based classification directly after chimera removal, then I need to deunique the “pick.pick.fasta” first?

Thanks
best,
Rich

2

Sorry, I’m not understanding your question - something got garbled following “Is cons.taxonomy…”

You really shouldn’t need to deunique your sequences; however, if you think you do, there is a deunique.seqs command.

Pat

3

Thank you for quick reply Pat
I repeat my question
I meant that is the output files from classify.otu command is deunique?
Second question if i need to use fasta file after chimera removal do i need to deunique it?

Thanks

4

If you include a name file or a count file (as we do in the SOPs), there’s no reason to deunique the data. You’ll notice that the deunique.seqs command is not used in the SOPs.

5

Pat,
I had a similar question about Deunique.seqs. I want to upload a fasta file with clean sequences (like we do in MiSeq SOP - remove chimeras, unwanted lineages, seqs with >8 homopolymer length etc) but with redundant sequences to MG-RAST for a tree visualization. In that case will using the Deunique.seqs with fasta=projectname…trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta (I did not have a mock community there is one pick less in the file name) and name =projectname.trim.contigs.good.name. Or can it take a count file (count =projectname.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.pick.count_table)?

Or is there an other way to get a fasta file with clean redundant sequences to upload to MG-RAST?

Thank you,
Indu

6

The count parameter will be added to the deunique.seqs command in our next release. Thanks for the feature request, :)!