Search found 497 matches

by kmitchell
Fri Jun 29, 2018 1:07 pm
Forum: mothur bugs
Topic: sequences not in group file but in fasta
Replies: 1
Views: 212

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: 102

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: 884

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: 279

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: 250

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: 283

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.
by kmitchell
Wed May 16, 2018 9:53 am
Forum: mothur bugs
Topic: make.contigs error with .gz fastq
Replies: 1
Views: 241

make.contigs error with .gz fastq

I'm getting unknown file format errors when I run make.contigs on .gz fastq. I've gotten this error in 1.40.1 (centos server) and 1.40.3 (both mac and linux desktop)
by kmitchell
Wed May 16, 2018 4:41 am
Forum: Commands in mothur
Topic: ITS reference alignment
Replies: 3
Views: 279

Re: ITS reference alignment

In general, ITS evolves too quickly to be aligned. If you are working with just a small taxonomic group, you could create you own alignment. But if you are working with all fungi, you can not align ITS/ITS2
by kmitchell
Tue Apr 24, 2018 6:57 pm
Forum: Commands in mothur
Topic: make.file and make.contigs " (2)" in fastq file names
Replies: 1
Views: 211

make.file and make.contigs " (2)" in fastq file names

I have some projects where I'm resequencing samples. I'd like to use sequences from both runs for the samples. make.file can't deal with the space, so I make the file.file by hand. Now make.contigs doesn't like that file because it looks like there are 5 columns. I'd rather not rename the files sinc...
by kmitchell
Tue Apr 24, 2018 11:43 am
Forum: Commands in mothur
Topic: Is there way to subsample multiple times?
Replies: 2
Views: 190

Re: Is there way to subsample multiple times?

I've thought about how to do this as well because it'd be nice to have a repeatedly subsampled shared file for things like indicator species analysis or species distribution modeling. But I and the few statisticians I've talked to haven't come up with a way to subsample without also hitting the 0 do...