Search found 29 matches

by gwidmer
Fri Jan 19, 2018 6:54 pm
Forum: Feature requests granted
Topic: generalized UniFrac distances
Replies: 3
Views: 8922

Re: generalized UniFrac distances

Hi Patrick, looks like it's been a while since you replied to this request. I was wondering whether a generalized UniFrac calculator is still on your to-do list. Thanks!
Giovanni
Tufts University
by gwidmer
Fri Nov 06, 2015 12:34 pm
Forum: Commands in mothur
Topic: classify.seqs with greenegenes tax and fasta gives 100% unclassified
Replies: 1
Views: 888

Re: classify.seqs with greengenes tax and fasta gives 100% unclassified

I can answer the question myself.. there was a memory issue and as a result one or multiple files created by classify.seqs: gg_13_5_99.gg.gg_13_5_99.8mer.numNonZero gg_13_5_99.gg.tree.train gg_13_5_99.gg.tree.sum gg_13_5_99.8mer were incomplete or otherwise corrupted. running classify.seqs in batch ...
by gwidmer
Thu Nov 05, 2015 3:12 pm
Forum: Commands in mothur
Topic: classify.seqs with greenegenes tax and fasta gives 100% unclassified
Replies: 1
Views: 888

classify.seqs with greenegenes tax and fasta gives 100% unclassified

Hi Pat and Sarah, I am trying to generate a biom file for picrust. I downloaded Gg_13_5_99.taxonomy.tar and opened it with $ tar -xvf Gg_13_5_99.taxonomy.tar when I run: classify.seqs(fasta=PhRats_84.subsample.chop.unique.good.filter.precluster.unique.fasta, name=PhRats_84.subsample.chop.unique.good...
by gwidmer
Sun Sep 21, 2014 7:44 pm
Forum: mothur bugs
Topic: ANOSIM: R values >>1
Replies: 1
Views: 3049

ANOSIM: R values >>1

Hi Pat and Sarah, I'm running the following command: anosim(phylip=SC_GP60_allelelength.dist, design=GP60.design, iters=100000) with the following input files: SC_GP60_allelelength.dist 10 Goat13 H34 81 Goat2 225 36 C1 576 225 81 C189 729 324 144 9 C245 900 441 225 36 9 C99 1089 576 324 81 36 9 L12 ...
by gwidmer
Fri Aug 01, 2014 12:28 pm
Forum: Commands in mothur
Topic: Mantel: order of samples in both matrices
Replies: 1
Views: 1872

Mantel: order of samples in both matrices

Hi Pat and Sarah,
I was wondering if Mantel expects that in the 2 matrices being compared, the samples are in the same order, that is rows and columns in both matrices are the same samples. In the env and veg files in the tutorial that's the case, but is it required?

thanks,

Giovanni
by gwidmer
Thu Apr 17, 2014 1:04 pm
Forum: Commands in mothur
Topic: interpretation of Lefse results
Replies: 1
Views: 2877

interpretation of Lefse results

Hi, I was wondering if anyone in the mothur community has found a way to functionally annotate the results from a Lefse analysis: I am comparing bacterial communities in two host species. I am identifying significantly different taxa using Lefse. At this point, I would like to functionally annotate ...
by gwidmer
Sun Mar 09, 2014 1:07 pm
Forum: mothur bugs
Topic: clearcut error and crashes
Replies: 3
Views: 6802

Re: clearcut error and crashes

Hi Sarah and Patrick: I ran into a similar problem with clearcut as Georgia posted in 2012" "Incorrect number of distance values on row" and "Syntax error in distance matrix at offset 3348507401". After reading your reply, I checked my filenames and found none shorter than 10 characters. Filenames r...
by gwidmer
Wed Jan 08, 2014 4:05 pm
Forum: Feature requests
Topic: archive of mock community taxonomy results
Replies: 2
Views: 4111

Re: archive of mock community taxonomy results

so how do we go about posting such data? I would be happy to provide classify.seqs results - or similar data - obtained from bacterial DNA controls.

Giovanni
by gwidmer
Mon Dec 23, 2013 1:39 pm
Forum: Feature requests
Topic: archive of mock community taxonomy results
Replies: 2
Views: 4111

archive of mock community taxonomy results

Hi Pat and mothur Community, I was wondering if there is any interest to create some kind of repository where people can upload taxonomy results obtained from sequencing mock bacterial communities. We routinely include the 20-species Microbial Mock Community B (BEI Resources cat no. HM-782D). Using ...
by gwidmer
Sun Sep 29, 2013 9:16 pm
Forum: mothur bugs
Topic: clearcut crashes mothur
Replies: 1
Views: 2359

clearcut crashes mothur

Hi Pat and Sarah, I'm having a problem with clearcut. Here is what happens when I enter the command: mothur > clearcut(phylip=WRF230413_31200.chop.unique.good.filter.phylip.dist) /cluster/home/g/w/gwidme01/.lsbatch/1380502661.379934: line 8: 32640 Aborted (core dumped) /cluster/tufts/gwidme01/mothur...