On September 22nd, OSC switched to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.

bam2fastq

bam2fastq is used to extract raw sequences (with qualities) from programs like SAMtools, Picard, and Bamtools.

Availability and Restrictions

Versions

The following versions of bam2fastq are available on OSC clusters:

Version Owens Pitzer
1.1.0 X* X*
* Current default version

You can use module spider bam2fastq to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

bam2fastq is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Genomic Services Lab at Hudson Alpha, Open source

Usage

Usage on Owens

Set-up

To configure your environment for use of bam2fastq, run the following command: module load bam2fastq. The default version will be loaded. To select a particular bam2fastq version, use module load bam2fastq/version. For example, use module load bam2fastq/1.1.0 to load bam2fastq 1.1.0.

Usage on Pitzer

Set-up

To configure your environment for use of bam2fastq, run the following command: module load bam2fastq. The default version will be loaded. To select a particular bam2fastq version, use module load bam2fastq/version. For example, use module load bam2fastq/1.1.0 to load bam2fastq 1.1.0.

Further Reading

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