Snakemake workflow for QC and processing of HIC data. Results in on .cool file and TAD calls for the data. All commands used to QC, and process hic-data are contianed in the main Snakefile.
Prep:
Place raw HIC reads in a new directory data/raw
mkdir -p data/raw
ln -s /path/to/some/data/*.fastq.gz data/raw/
Configure the file: src/config.yml
Generate Arima HIC genome restriction site file using the hicup command hicup_digester with the flag --arima for compatability with the Arima HIC protocol.
All commands used to QC, and process hic-data are contianed in the main Snakefile. The pipeline uses conda for dependency management. Make sure you have installed a recent version of snakemake and conda.
Execution:
snakemake --use-conda -j20
Runtime
The hicup pipeline is the most resource intensive step that can be expected to run for at least 24 hours for a sample with a sequencing depth of 500 million reads and 8 threads.