Search found 501 matches

by kmitchell
Tue Aug 28, 2018 11:34 am
Forum: Commands in mothur
Topic: aligning fungal ITS sequences for pre.cluster?
Replies: 1
Views: 124

Re: aligning fungal ITS sequences for pre.cluster?

I've been grappling with this as well (my last project with ~40 samples too 9 days on our cluster). I know some fungal labs that been using dada2, but I haven't played with that yet. Given how little foundation we have for determining what is a useful OTU level for a non-coding region in fungi, I'm ...
by kmitchell
Fri Aug 03, 2018 4:41 pm
Forum: Commands in mothur
Topic: aligning sequences to SILVA bacterial reference database
Replies: 1
Views: 181

Re: aligning sequences to SILVA bacterial reference database

it's a warning, not an error so you may not need to do anything.

the ones that eliminated too many bases are likely bad though that's a pretty big number so I'd be a little suspicious. flipping the seqs is usually fine unless you know that your seqs are all 5'->3'
by kmitchell
Fri Aug 03, 2018 4:30 pm
Forum: Theory behind mothur
Topic: Contigs larger than expected
Replies: 1
Views: 386

Re: Contigs larger than expected

I usually toss any seq with N, so most of the big ones would be tossed in my processing.
by kmitchell
Fri Jun 29, 2018 1:07 pm
Forum: mothur bugs
Topic: sequences not in group file but in fasta
Replies: 2
Views: 521

sequences not in group file but in fasta

I'm getting an error I've never seen before. make.contigs seems to work, but some sequences aren't getting into the groups file? For one dataset I saw this with 1.39.5, switched to 1.40.5 and it went away. Second dataset, still seeing it in 1.40.5. I'll send logfiles to mothur bugs

thanks Kendra
by kmitchell
Wed Jun 20, 2018 11:55 am
Forum: Commands in mothur
Topic: how to get mothur to read files from a portable hard drive
Replies: 1
Views: 216

Re: how to get mothur to read files from a portable hard drive

USB probably isn't fast enough to read/write files. several steps in the sop (alignment and dist esp) will generate very large files, you should try to find a bigger computer to process these files on.
by kmitchell
Thu May 31, 2018 12:41 pm
Forum: Theory behind mothur
Topic: Subsampling 3 different groups at same level
Replies: 5
Views: 1157

Re: Subsampling 3 different groups at same level

It's taking 4 days to subsample? I'd be surprised with even 2 days for hundreds of mouse samples (I run on 32 cores). Are you following the SOP including the unique.seqs and pre.cluster steps? What is this data? MiSeq 2x250 or somthing else?
by kmitchell
Fri May 25, 2018 1:12 pm
Forum: Commands in mothur
Topic: ITS reference alignment
Replies: 3
Views: 418

Re: ITS reference alignment

sorry, missed your followup. I do use ITS2 even though we can't align it. It gives the best taxonomic resolution that we can get for all fungi. If you are working with specific groups of fungi, you may want to choose a different target.
by kmitchell
Thu May 24, 2018 1:26 pm
Forum: Feature requests
Topic: make.file with inputdir printing inputdir
Replies: 1
Views: 375

make.file with inputdir printing inputdir

Somewhere between 1.38 and 1.40 the behavior of make.file when using inputdir changed. in 1.38 the resulting file would be sample1 inputdir/sample1_R1.fastq.gz inputdir/sample1_R2.fastq.gz in 1.40 it's sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz Is there a flag that I'm missing that will control...
by kmitchell
Thu May 24, 2018 1:03 pm
Forum: mothur bugs
Topic: classify.otu: dissapering Salmonella
Replies: 7
Views: 442

Re: classify.otu: dissapering Salmonella

I bet vsearch is your issue. Salmonella is low abundance right? so it's not being used to seed any clusters, it's being added into clusters which depending on how they were seeded could be other Enteros which is why the otu's are Entero unclassified.