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Questions tagged [qiime]

QIIME is an open source software package for comparison and analysis of microbial communities.

QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

QIIME allows analysis of high-throughput community sequencing data.

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A Utf8 encoded file produces UnicodeDecodeError during parsing

I'm trying to reformat a text file so I can upload it to a pipeline (QIIME2) - I tested the first few lines of my .txt file (but it is tab separated), and the conversion was successful. However, when I try to run the script on the whole file, I…
A. Alex
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Pointing qiime to path containing R-related program

I've installed a program from a .tar.gz package (biom, because even though it's outdated I need it for a qiime script). Problem is that when I run the qiime script, R is looking in different sources (/home/username/R/x86_64-pc-linux-gnu-library/3.4,…
Austin McDonald
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QIIME2 on Docker : no space left on device (although there is)

I want to analyse data with QIIME2 on a Docker container. Note that this is my first time with Docker. I created the image and then the container, and started to analyse a small subsample of data with success. However, one step of the pipeline…
Flamingo
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R-script, issue with data_path <- paste

This is the top of my R script which was shared on qiime forums. The script is meant to make a metadata file for multiple fastq files. How do I edit it to run without needing editing every time but I cant seem to tell it to use the current working…
Gus Bishop
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python bokeh legend out of the plot size

I'm new in python, and somebody help me with this code, but I want to change some parameter: First the size of the legend out of the plot, some time the legend are to big (example:…
abraham
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User input in subprocess.call

I am writing a program to automate some qiime2 commands. I want to incorporate user input. So far, I have: # Items to import import subprocess from sys import argv #Variables format=argv[1] # Import sequences for Phred33 format if…
Jessica
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Removing lines from barplot in R

I have created a barplot for metagenomic data using RStudio plot_bar(mp3, "Sampletype", fill = "Family", title = title) But I am getting lines inside the bar.I need clear bars without any lines. How to do it? library("phyloseq");…
Kiran
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if then bash statement does not work with qiime commands

I just started to bash and I have been stuck for sometime on a simple if;then statement. I use bash to run QIIME commands which are written in python. These commands allow me to deal with microbial DNA. From the raw dataset from the sequencing I…
Anaïs Larue
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How do you plot rarefaction plots by sampling sites?

Simplified version of my problem: I have an OTU table with with 60 sample points (each with abundances for various OTUs) across three sites: A, B and C. Each site has 20 samples. I want to plot rarefaction curves for each of the sites: A, B and C. I…
Frodo Baggings
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match with 2 or more options perl

I have two formats obtained from qiime analyses, one obtained from silva database and other obtained from GreenGenes. The difference among those files, are that silva files have a progressive D_number for each taxon (kingdom= D_0__, phylum= D_1__,…
abraham
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Reshape very large OTU (abundance) table in wide to long format - 400,000 observations

I have a very large OTU (abundance) table. There are over 100 samples and 4000 observations per sample (4000 taxa). An example of the OTU table is here: #OTUID 1 2 3 4 5 6 7 8 OTU1 0 0 0 0 0 3 0 0 OTU2 0 0 0 …
user3105519
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Calculate Spearman correlation Rho using cor between paired samples between two matrices

I'm having some problems with trying to run cor.test, based on two OTU tables (essentially an abundance matrix). I have a table with 8 different sampling spots (columns 1 to 44) and for each sampling spot I measured a variable (VARIABLE1, first row)…
user3105519
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running matplotlib with no DISPLAY

When matlplotlib run (from summarize_taxa_through_plots.py) I got the error: ... raise RuntimeError('Invalid DISPLAY variable') RuntimeError: Invalid DISPLAY variable I saw this problem in a lot of sites, the solution is to change user's…
user1980099
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How to assign taxonomy to trnL sequences using BLAST

I am using the trnL chloroplast gene to identify plants from herbivore dung, and am currently trying to assign taxonomy to trnL sequences from my Illumina output. Here is the QIIME script and options I would like to run: assign_taxonomy.py -i…
HerbivoreGuy
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Downloading Qiime to CentOS6.4. Having problems with python version

I'm trying to download Qiime to CentOS 6.4. and having troubles with the version of python. I have not much experience dealing with Linux system. I've already downloaded python 2.6.6 in /usr/bin/python and I think this is the default version of…
S. Hokyung
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