Comments (3)
Thank you for using the material. We do not use Kraken in the lesson since because of RAM limitations some laptops won't be able to run it. For that reason, we provide the report files from Kraken, and you only will need kraken-biom. Anyway, here is the biom file, which also should be available for future versions of the data in zenodo
https://github.com/carpentries-incubator/metagenomics/blob/gh-pages/files/cuatroc.biom
Some notes:
-
The kraken output files are on the zenodo data as indicated in the data section
https://carpentries-incubator.github.io/metagenomics-workshop/data/index.html -
The software can be installed using the yml specifications file indicated in the setup section
from metagenomics-analysis.
Thank you for sharing the BIOM file! I just noticed that I had been looking at the setup page for the genomics workshop (https://datacarpentry.org/genomics-workshop/setup.html) instead of the one for the metagenomics workshop (https://carpentries-incubator.github.io/metagenomics-workshop/setup.html). My bad! I see the metagenomics setup page indeed includes all the software packages and a conda YAML file. That should settle the issues I ran into. Sorry if I caused some confusion.
from metagenomics-analysis.
Please if you have time, let us know if the setup works for you. Thank you for using the lesson.
from metagenomics-analysis.
Related Issues (20)
- Data processing and visualization too dense HOT 2
- Improve Assessing Read Quality episode HOT 1
- Improve Trimming and Filtering episode HOT 1
- Provide files created during the lesson HOT 2
- Exercises and discussions in Data processing lesson HOT 1
- Typos HOT 2
- Required software setup section HOT 4
- R no despliega graficas HOT 5
- Add explanation about factors in Intro to R
- Adapter files HOT 1
- Database for taxonomic assignment
- Add "not spaces in file names" in the Data tidiness
- metadata
- RStudio not working in AWS HOT 1
- Quast HOT 1
- Review the Kraken command HOT 1
- Say something about the thrid sample
- The AMI is dirty HOT 4
- How to recreate kraken results? Which database? HOT 1
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from metagenomics-analysis.