Software: how_are_we_stranded_here
Description
How_are_we_stranded_here is a python package for testing strandedness of RNA-Seq fastq files.
Available Versions
| Unspecified: | 1.0.1 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/how_are_we_stranded_here and its home page on Github.
Commands
- check_strandedness
Module
You can load the modules by:
module load biocontainers
module load how_are_we_stranded_here
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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