Any tutorial contained a example data can be downloaded?

[Wang cs001632]

https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-(IMPACTT-December-2022)-Taxonomic-annotation

For example, it is a good tutorial, however, no example fastq can be downloaded.

[Andre Comeau]

We are currently working on this and the files may become available soon as links on that tutorial Github page.

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
​	Research Associate (Lab Manager) Morgan Langille Lab • Dept. of Pharmacology ResearchGate Profile • GoogleScholar Publications
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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of Wang cs001632 <cs00...@gmail.com>
Sent: Tuesday, December 13, 2022 12:05 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] Any tutorial contained a example data can be downloaded?

 

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https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-(IMPACTT-December-2022)-Taxonomic-annotation

For example, it is a good tutorial, however, no example fastq can be downloaded.

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[Robyn Wright]

Hi there,

Although I haven't had a chance to update the material yet, the data for the June 2022 IMPACTT workshop can be downloaded. If you follow this tutorial, it gives you instructions on downloading the data and setting up the environment/installing the tools that you will need for the tutorial, outside of the IMPACTT workshop. For the taxonomic section, the only thing that I added for December was a script for generating a heatmap with the data at the end (plot_bracken_output.py, attached). 

Let me know if you have other questions!

Robyn

[Wang cs001632]

Thank you for your timely reply. I used to run microbiome helper at virtual box on PC, however, it became complicated in server.

https://github.com/LangilleLab/microbiome_helper/wiki/Metagenomics-(taxonomic-annotation;-IMPACTT-2022)

I believe you have prepared a small dataset to test this tutorial. Could you kindly sent it to me. cs00...@gmail.com

Thanks.

[Robyn Wright]

Yes, the link is in step 7 of the initial instructions to set up the environment and download the data for those going through the tutorial that are not in the IMPACTT workshop. The fastq files and all other files needed for going through the tutorial are in there. They are all zipped together in a file on Dropbox here (the tutorial provides commands for download), but the files far too big for me to send you via email – you will need to download them from Dropbox, and I recommend that you follow the instructions at the start of the tutorial so that you have all of the other packages recommended.

 

Typically, the analysis of metagenomics data requires more memory than a desktop computer has and we therefore haven’t provided a virtual box for this part of the analysis. With the instructions for also installing the packages required, you’ll more easily be able to run this pipeline on your own data afterwards.

 

Robyn

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