How_are_we_stranded_here

Introduction

How_are_we_stranded_here is a python package for testing strandedness of RNA-Seq fastq files.

For more information, please check its website: https://biocontainers.pro/tools/how_are_we_stranded_here and its home page on Github.

Versions

1.0.1

Commands

check_strandedness

Module

You can load the modules by:

module load biocontainers
module load how_are_we_stranded_here

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 How_are_we_stranded_here on our clusters:

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

module --force purge
ml biocontainers how_are_we_stranded_here

check_strandedness --gtf Homo_sapiens.GRCh38.105.gtf \
    --transcripts Homo_sapiens.GRCh38.cds.all.fa \
    --reads_1 seq_1.fastq  --reads_2 seq_2.fastq