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 Oakley owens
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 without restriction.

Usage

Usage on Oakley

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 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.

Further Reading

Service: 
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