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