Sample grouping in Metagenomics Analysis in Galaxy

Question: Sample grouping in Metagenomics Analysis in Galaxy

3.3 years ago by

ewhameta • 0

Korea, Republic Of

ewhameta • 0 wrote:

I have 20 Fastq files from 16S rRNA Illumina run.

I am trying to learn how to analyze these data.

1. Could someone recommend a complete workflow for metagenome analysis in Galaxy?

2. The 20 files are from 2 groups of patients (n=10) and normal control (n=10). During an analysis (galaxy workflow), when is the best time to group files into a 'patient' or 'mormal'.

Thanks

Sangh

galaxy • 1.2k views

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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by ewhameta • 0

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

An updated protocol for this analysis is pending publication to the Galaxy NGS 101 suite of tutorials. Follow that wiki for updates.

Meanwhile, the metagenomics tutorial from GVL could help you to get started. Please see this prior Q&A for links: metagenome analysis in Galaxy

Best, Jen, Galaxy team

ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer;

Your e-mail has been of great help.

I followed a link you posted before; Tutorials from the GLV have one for 16S metagenomics that appears to be good match: http://galaxy-qld.genome.edu.au/workflow/list_published

One more thing I need is 1. I have 10 metagenome Illumina data (i.e., 10 fastq files) for "healthy" and 10 for "disease"; 2 groups 2. In the above workflow, I was able to find all the steps for individual file-based analysis. 3. I want to 'group' the samples into 2 ('healthy' and 'disease') for differential analysis; and this step I couldn't find. 4. The author of the workflow "qfab'; how can I reach this person and ask questions about grouping. e-mail address? 5. Or could you tell me how?

Sincerely

Sanghwa Yang Professor Ewha University, Seoul, Korea

2015-08-01 2:47 GMT+09:00 Jennifer Hillman Jackson on Galaxy Biostar < notifications@biostars.org>:

ADD REPLY • link written 3.3 years ago by ewhameta • 0

Let me re-elaborate my question;

In Cuffdiff of RNA-seq, we can set conditons ('groups' as I wrote before) and then add multiple samples as 'replicates'. Can I do that in metagenomics?

Thanks Sanghwa Yang

2015-08-27 12:42 GMT+09:00 Sh Yang <ewhameta@gmail.com>:

ADD REPLY • link written 3.3 years ago by ewhameta • 0

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