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Questions tagged [mothur]

mothur is an open source software package aims to provide tools to analyze and process microbial community and ecology, and bioinformatics data.

12 questions
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1 answer

R package reshape function melt error: id variables not found in data when working with a lot of factors

I am working with a rarefaction output from mothur, which basically gives me a dataset containing the number of sequences sampled and the number of unique sequences in several samples. I would like to use ggplot2 to visualize this data and therefore…
FM Kerckhof
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Convert/transform an abundance (OTU) table/data.frame (to a fasta file) in R

I'm working on a large dataset at the moment and so far I could solve all my ideas/problems via countless google searches and long try & error sessions very well. I've managed to use plyr and reshape functions for some transformations of my…
plik
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2 answers

unable to import a mothur tree into R

I build a tree by mothur, it produced a newick format file here is the tree file…
louyi871
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Include command screen output in GNU Parallel log report

I have one script calling another multiple times with GNU Parallel. Here is the important part of my parallelization code: export PTH_data={my input path} export WDIR={my output path} export idsuffix=\.'[1-2]' export R1=${idsuffix/\[1-2\]/1} export…
ALG
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How to generate an ordination plot from a distance matrix in R

Here I have another 'graphical' problem: I have obtained from MOTHUR the following distance matrix (coming from a weighted unifrac analysis): 20 F3D0 F3D1 0.222664 F3D141 0.157368 0.293308 F3D142 0.180278 0.319198 …
mafernandez
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1 answer

R: calling a system command

I was trying to invoke an executable from within R code using the system command. If I use command line in a terminal to invoke R, and then execute system("mothur"). However, if from within an R script (on RStudio) I execute the same command, I get:…
bsmith
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Question on Mothur classify.seqs : Sequence not found in taxonomy file

Hello I've been getting this issue and I'm not sure how to fix it. I'm currently running the following command on mothur: classify.seqs(fasta=all.good.unique.good.filter.unique.abund.pick.fasta, count=…
Axolotl Boricua
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AttibuteError when trying to make configs

AttributeError: module 'collections' has no attribute 'Sequence' i get this error everything i try to run my code but there isn't any information about how to use Mothur except for the the documentation. `# python3 import sys import queue import…
Omolewa Oreweme
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I started to using mothur version - v.1.36.1-, but I got some error messages (shown below). How I can overcome this?

I start the Mothur Tutorial (https://www.mothur.org/wiki/MiSeq_SOP). But from the beginning, I got some error messages when I create " make.file "in mothur*(Error commands are shown below). I changed parameters but the result was negative. How can I…
Jay
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1 answer

Tax4Fun - Error length of 'dimnames' [1] not equal to array extent

I'm attempting to run Tax4Fun to predict functional capabilities from 16S data. As the analysis up to this point was carried out in Mothur, I could not use biom as an input (incompatibility between biom versions, which I knew about beforehand). I…
Sophie Shaw
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Merge by average and plot alternate data from table

I used estimateR (vegan) to generate this table from mothur outputs. However, so far, I am unable to go on with this, being that I am not aware of how to plot from tables... row.names ALG.1 ALG.2 ALG.3 ALG.4 ALG.4 ALG.5 ALG.6 ALG.7 …
André Soares
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Output selected lines from a file as the first column and the file name as the second coulmn

I just recently started to use powershell in win7 in order to produce pipeline like scripts for the program mothur. Before I used bash scripting in ubuntu to do this. I am happy that everything works well now except one task: I would like to like to…
user2251977
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