strique.rst

Strique

Introduction ~~~~~~~~ STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data.

For more information, please check:
Docker hub: https://hub.docker.com/r/giesselmann/strique
Home page: https://github.com/giesselmann/STRique

Versions

• 0.4.2

Commands ~~~~~~~ - STRique.py - STRique_test.py - fast5Masker.py

Module

You can load the modules by:

module load biocontainers
module load strique

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run strique on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=strique
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers strique

STRique_test.py
STRique.py index data/ > data/reads.fofn
cat data/c9orf72.sam |  STRique.py count ./data/reads.fofn ./models/r9_4_450bps.model ./configs/repeat_config.tsv --config ./configs/STRique.json