/sTeloMap

Pipeline for the identification and characterization of telomere-related small RNAs (telo-sRNAs)

Primary LanguagePythonMIT LicenseMIT

Pipeline for analysis of telomere-related small RNAs (telo-sRNAs)

This pipeline searches for reads that map to telomeres with up to three mismatches. Results are stored in an sqlite3 database which contains sequence data and sample metadata.

Installation

git clone https://github.com/sfrenk/sTeloMap.git
cd sTeloMap
bash install.sh

Usage

  1. Use setup_working_dir.sh to set up the working directory for analysis:
setup_dir.sh -d <directory containing reads>
  1. Run the snakemake script
bash run_snakemake.sh
  1. Merge results databases
python3 merge_db.py -o <merged db name> <list of dbs to merge>