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
Service:
Fields of Science:
