bam2fastq

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

Availability and Restrictions

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 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

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