On Thu, Dec 16, 2010 at 1:48 PM, Marina Gourtovaia <mg8@sanger.ac.uk> wrote:
Thanks a lot for the tip, Peter. Also, had to use a different filter expression (sPaired is True)
Great.
BTW, I am making a wrapper around Picard http://picard.sourceforge.net/command-line-overview.shtml#Overview. Is there enough interest to this to submit this to the core Galaxy? In Sanger, our Illumina pipeline end up with BAM files, so the end users need a BAM-FASTQ converter, hence this binding I am making
I'm sure a Picard wrapper would be useful. For this particular case, BAM to unaligned FASTQ you may have other options. I'd take a look at pysam, the Python wrapper for the samtools C API if I were you, but then I don't speak Java ;) Also EMBOSS has some BAM support nowadays, and I've got some experimental code on a Biopython branch which was partly written for recovering unaligned paired end FASTQ files from BAM in order to remap them to a different reference. Peter