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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.