Search found 3145 matches

by pschloss
Mon Sep 17, 2018 2:30 pm
Forum: Commands in mothur
Topic: make.contigs w/ oligos file
Replies: 2
Views: 37

Re: make.contigs w/ oligos file

If you run "head" on the first few lines of the outputted fasta file, do you see the oligos? If they made it through the command then they should have been found and removed.

Pat
by pschloss
Thu Aug 30, 2018 2:07 pm
Forum: mothur bugs
Topic: 0 sequences removed after remove.seqs
Replies: 2
Views: 269

Re: 0 sequences removed after remove.seqs

Sorry for not getting to this earlier... I think the problem is you left out the dereplicate=T in the reference based approach. When you leave it out, it automatically takes the sequences out of the fasta file.
by pschloss
Tue Aug 07, 2018 11:42 am
Forum: mothur bugs
Topic: aligning sequences to SILVA bacterial reference database
Replies: 1
Views: 222

Re: aligning sequences to SILVA bacterial reference database

Is it possible that you sequenced your fragments in the reverse direction or that you flipped them earlier in the pipeline? The warning indicates that the sequences were flipped to the correct orientation in align.seqs, so you should be in good shape.

Pat
by pschloss
Mon Jul 16, 2018 1:38 pm
Forum: Feature requests
Topic: data files with frequency values
Replies: 1
Views: 635

Re: data files with frequency values

Hi - we haven't run into this. Sounds liek you would need to extract that informatino to make a count file

Pat
by pschloss
Mon Jul 09, 2018 12:55 pm
Forum: Commands in mothur
Topic: Compare models for AMOVA
Replies: 1
Views: 214

Re: Compare models for AMOVA

Hi Eric,

You can make multiple design files and then run amova with each. That shouldn't be a problem.

Pat
by pschloss
Mon Jul 09, 2018 12:54 pm
Forum: mothur bugs
Topic: sequences not in group file but in fasta
Replies: 2
Views: 521

Re: sequences not in group file but in fasta

Can you tell us how you're running make.contigs and what OS you're using?
by pschloss
Mon Jul 09, 2018 12:53 pm
Forum: Commands in mothur
Topic: new make.contigs
Replies: 3
Views: 301

Re: new make.contigs

Oh - not at this time.
by pschloss
Mon Jun 25, 2018 4:20 pm
Forum: Commands in mothur
Topic: new make.contigs
Replies: 3
Views: 301

Re: new make.contigs

Hmmm... not sure I know what you mean - make.contigs hasn't really changed the output fasta sequence data since the Kozich paper was published.

Pat
by pschloss
Mon Jun 18, 2018 4:18 pm
Forum: mothur bugs
Topic: segmentation fault - make.contigs
Replies: 1
Views: 244

Re: segmentation fault - make.contigs

Can you update your version of mothur? That's a few years old - we're up to 1.40 now and I suspect these bugs may have been fixed in the mean time.

pat
by pschloss
Mon May 21, 2018 2:44 pm
Forum: Commands in mothur
Topic: non-sequence data
Replies: 1
Views: 284

Re: non-sequence data

Sure - shouldn't be a problem.
Pat