Allele-specific expression (ASE) for short tandem repeats (STRs)
Execute the following command.
git clone https://github.com/aryarm/str_ase
Example data for the pipeline is also available for download upon request.
The pipeline is written as a Snakefile which can be executed via Snakemake. For reproduciblity, we recommend installing version 5.30.2:
conda create -n snakemake -c conda-forge --no-channel-priority 'bioconda::snakemake==5.30.2'
We highly recommend you install Snakemake via conda like this so that you can use the --use-conda flag when calling snakemake to let it automatically handle all dependencies of the pipeline. Otherwise, you must manually install the dependencies listed in the env files.
-
Activate snakemake via
conda:conda activate snakemake -
Execute the pipeline on the example data
Locally:
./run &
Log files describing the output of the pipeline will be created within the output directory. The log file contains a basic description of the progress of each rule, while the qlog file is more detailed.
You must modify the config.yaml file to specify paths to your data before you perform step 2 above. Currently, the pipeline is configured to run on our example data.
We recommend that you run snakemake --help to learn about Snakemake's options. For example, to check that the pipeline will be executed correctly before you run it, you can call Snakemake with the -n -p -r flags. This is also a good way to familiarize yourself with the steps of the pipeline and their inputs and outputs (the latter of which are inputs to the first rule in each workflow -- ie the all rule).
Note that Snakemake will not recreate output that it has already generated, unless you request it. If a job fails or is interrupted, subsequent executions of Snakemake will just pick up where it left off. This can also apply to files that you create and provide in place of the files it would have generated.
By default, the pipeline will automatically delete some files it deems unnecessary (ex: unsorted copies of a VCF). You can opt to keep these files instead by providing the --notemp flag to Snakemake when executing the pipeline.
A Snakemake pipeline defining rules for every step of the analysis.
Defines options and input for the Snakemake pipeline.
An example bash script for executing the pipeline using snakemake and conda. Any arguments to this script are passed directly to snakemake.
Conda environment files for the dependencies of our pipeline.
Example data for the pipeline, which is available upon request. You can also generate your own using the prepare pipeline.
Snakemake rules used by the pipeline. See the rules README for more information about each file.
Various scripts that are utilized within the pipeline. See the scripts README for more information about each file.