hurwitzlab/bowtie-samtools

Name: bowtie-samtools

Owner: Hurwitz Lab

Description: Runs bowtie2 and samtools on stampede2, Part two of Radcot

Created: 2018-04-20 21:04:35.0

Updated: 2018-05-15 20:43:52.0

Pushed: 2018-05-15 20:43:51.0

Homepage: null

Size: 196

Language: Python

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README

centrifuge-patric - Radcot Part One - 1st step

• Identified bacterial species from a metagenomic sample
• Downloaded genomes of said species

bowtie-samtools - Radcot Part Two - YOU ARE HERE

• Quantify transcripts of genes within these species

cuffdiff-keggR - Radcot Part Three - 3rd step

• Annotate RNA counts of genes with KEGG pathway information
• Generate graphs of RNA count differences per KEGG module

How to use:

1. Use https://www.imicrobe.us/#/apps to access the app with your cyverse login OR
2. git clone https://github.com/hurwitzlab/centrifuge-patric on a linux system where you have admin rights
3. Install singularity
4. Build the singularity image in /singularity/ by executing make img
5. Upload all the files to a HPC with a slurm scheduler¹
6. Run the program with sbatch run.sh [arguments]

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¹I assume this can be adapted to run on other batch-scheduled high-performance computer systems but this has not been tested.