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Welcome to the rna-seq-pop wiki!

Usage

If you use this workflow in a paper, don't forget to give credits to the author by citing the URL of this (original) repository and, if available, its DOI (see above).

Step 1: Obtain a copy of this workflow

1. Create a new github repository using this workflow as a template.
2. Clone the newly created repository to your local system, into the place where you want to perform the data analysis.
3. As the workflow contains submodules (compkaryo & mpileup2readcounts), git clone --recursive should be used to clone the repo.
4. If you want to run the differential SNPs analysis, please compile mpileup2readcounts by navigating to its folder in workflow/scripts and: g++ -std=c++11 -O3 mpileup2readcounts.cc -o mpileup2readcounts

Step 2: Configure workflow

Configure the workflow according to your needs via editing the files in the config/ folder. Adjust the example config.yaml to configure the workflow execution, and samples.tsv to specify your sample setup. Information on how to setup the configuration file can be found in the config README config/README.md, as recommended by snakemake best practices.

If you are using the workflow and would like to give feedback or troubleshoot, consider joining the discord server here