Job script:
#!/bin/bash
#SBATCH --job-name=rfee
#SBATCH --workdir=/home/user.name/rfee/
#SBATCH --output=r_foreach_example_console_output.txt
#SBATCH --mem-per-cpu=100 # specify RAM per CPU here in Mb
#SBATCH --time=0:02:00
Job script:
#!/bin/bash
#SBATCH --job-name=rfee
#SBATCH --workdir=/home/user.name/rfee/
#SBATCH --output=r_foreach_example_console_output.txt
#SBATCH --mem-per-cpu=100 # specify RAM per CPU here in Mb
#SBATCH --time=0:02:00
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)