I have a microbiome dataset and I am trying to compare different groups of mice (symptomatic animals, asymptomatic animals and a control group).
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[Microbiome] Core Compare
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Interested in Metabarcoding?
Course "16 S/ITS Metabarcoding of microbial communities"
https://www.physalia-courses.org/courses-workshops/... -
Qiime Ubuntu Command Line File Name Code?
After running multiple_join_paired_ends.py on my 600 Illumina MiSeq files, the output leaves each sample in individual folders. The folder has a unique... -
Fastx-Toolkit - Analyze multiple files in directory (Linux/Qiime)
I am trying to run the fastq_quality_filter on a directory of .fastq files (~500) where each file has a unique name. I simply cannot get it to work on... -
Qiime vs illumina basespace 16s pipeline, Which is better?
Hello everyone, we currently handle a 16 project which analyzed by QIime and illumina basespace 16s app. The results are quite different. I googled and... -
Using DeSeq2 in R or Qiime to examine taxonomic rank other than OTU level
Hello,
I am trying to follow the example given here https://github.com/joey711/phyloseq/issues/683, using DeSeq2 to examine differential... -
Python commands not found at all in QIIME
Hello all,
I am very new to qiime, and bioinformatics in general. I'm going to try and explain this the best that I can, but if something... -
Issue with FASTA header in QIIME
Dear all,
I have to analyze a set of 26 samples of 16S amplicon data, coming from 250 nt Paired-end Illumina Hi-Seq reads. When I received... -
alpha diversity on collapse biom table
Hi,
I am trying to run alpha diversity on biom file obtained by collapsing_sample.py. alpha and beta diversity gives only 0 or nan in... -
Newbie to MiSeq, QIIME workflow question
Hi all,
I just got my MiSeq data for fungal ITS sequences in a large number of samples. I am going to be using QIIME to do the analysis... -
Gaurav_genomics started a topic Hello All.I have annotated my metagenomic dataset using MG-RAST and now want to generin MetagenomicsHello All.I have annotated my metagenomic dataset using MG-RAST and now want to gener
I have annotated the Metagenomic dataset using MG-RAST and now I want to generate the ".tree" phylogenetic tree file that can be further given... -
how to remove first 15 bases of a sequence using unix or qiime
So I'm pretty sure all of my sequences have a 15 base pair adaptor sequence at the beginning, and I'd like to remove it, so then my downstream analysis... -
15bp mystery sequence at the beginning of 454 data
Hello-
So I am working on replicating an analysis from a published study that used 454 sequencing with titanium chemistry, and have downloaded...Last edited by Brian Bushnell; 05-13-2015, 09:54 AM. -
guidelines with 16s RNA data
Hello Members, and Seniors,
I don't have any experience in/on 16s RNA data.
I know there are tools like QIIME, and mothur which do...Last edited by bio_informatics; 05-01-2015, 04:55 AM. -
PAN and CORE genome analysis
Hi,
I have an OTU biom file (obtained from Closed reference QIIME 1.8.0 v) contains 65 samples, I am trying to do analysis for PAN/CORE genome....
