#5 srf2fastq.c: Sequentially outputting paired-end data

Accepted
closed-accepted
None
5
2009-11-24
2009-11-18
Jordan Mendler
No

Some aligners, such as Bfast (https://secure.genome.ucla.edu/index.php/BFAST), require fastq input for paired-end data to be in sequential records within a single file. For instance, the fastq should look like:
@read1, end 1
....
@read1, end 2
....
@read2, end 1
...
@read2, end 2

I have attached a patch for srf2fastq to add a -S option to do this. It outputs to stdout as usual, except outputs one region at a time, rather than joining multiple regions.

Discussion

  • James Bonfield
    James Bonfield
    2009-11-24

    Applied to the svn repository and so will be in the next release. Thanks.

     
  • James Bonfield
    James Bonfield
    2009-11-24

    • milestone: --> Accepted
    • assigned_to: nobody --> jkbonfield
    • status: open --> closed-accepted