bowtie2 Specifying Read Groups

2011-12-15
2013-06-05
  • Nathan S. Watson-Haigh

    According to the documentation, I can specify read groups for SAM output using -sam-rg. However, I can't for the life of me get this to work! It simply returns to the prompt without any output (see command below).

    If I'm doing something obviously wrong, could you provide an example of how to do this?

    cat $data/454_symlinks/se/*.fastq   | bowtie2 -sam-rg "ID:$file-shotgun454" -sam-rg "SM:AH-E" -sam-rg "LB:Shotgun" -sam-rg "PL:454" -threads 25 -x $file - -S $file-shotgun454.bowtie2.sam

    Cheers,
    Nathan

     
  • Ben Langmead

    Ben Langmead - 2011-12-19

    Nathan,

    You're 100% right - there was a silly bug that was causing a segfault when users would specify -sam-rg.  This is fixed in the trunk and the fix will be present in the next version (2.0.0-beta6).

    Thank you!
    Ben

     
  • Nathan S. Watson-Haigh

    Where can I get my hands on the sourcecode for bowtie2?

     
  • Daniel Swan

    Daniel Swan - 2012-04-24

    Can I just add the request for access to the source code - if things have been fixed in a repository somewhere I'm prepared not to wait for a bundled release to get my hand on some fixes.

     

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