Bedtools
Program description:
Collectively, the bedtools utilities are a swiss-army knife of tools for a
wide-range of genomics analysis tasks. The most widely-used tools enable
genome arithmetic: that is, set theory on the genome. For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as
BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a
relatively simple task (e.g., intersect two interval files), quite
sophisticated analyzes can be conducted by combining multiple bedtools
operations on the UNIX command line.
Versions:
Name: bedtools Version: 2.21.0 Platform: x86_64 Category: Applications/Engineering URL http://bedtools.readthedocs.org/en/latest/index.html Provides: bedtools
Below is how to load the module into the software:
Module loading reference
Sample SLURM runtime script:
#!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks-per-node=4 #SBATCH --mem=4gb #SBATCH --time=01:00:00 # Set paths or load appropriate modules module load bedtools module load gcc # Set the $TMPDIR variable export TMPDIR=$HOME/grant_$SLURM_JOB_ACCOUNT/scratch/$USER/$SLURM_JOB_ID # We set application variables export SCR=${TMPDIR} # We set auxiliary variables INPUT_DIR="input" OUTPUT_DIR="output" OUTPUT_FILE="OUTPUT" # Create a temporary directory mkdir -p ${TMPDIR} # Copy the input data to the directory pointed to by the $TMPDIR variable cp ${SLURM_SUBMIT_DIR}/${INPUT_DIR}/* ${TMPDIR} # Go to the $TMPDIR directory cd $TMPDIR # We do the calculations bedtools intersect -a cpg.bed -b exons.bed | head -5 > result.txt # Footer cat << EOF -------------------------------------------------- --------------- End of calculations [$(date)]. -------------------------------------------------- --------------- EOF # We finish the calculations, copy the contents of the $TMPDIR/output directory # to the directory from which the job was queued. mkdir $SLURM_SUBMIT_DIR/${OUTPUT_DIR} cp -r $TMPDIR/* $SLURM_SUBMIT_DIR/${OUTPUT_DIR}/ # Clear working directory rm -rf $TMPDIR
Below are the files that should be in the input directory.
File:Bedtools input.zip