On Tue, Nov 4, 2014 at 2:44 PM, Peter Cock <[email protected]> wrote: > Hi all, > > I'm looking for a little advice on the pre-existing SAM/BAM filtering > tools already in the Galaxy Tool Shed (to avoid reinventing the wheel). > > As I mentioned on another thread, I'm working on a wrapper for the > "samtools bam2fq" command (targeting samtools 1.1 which fixed > some bugs in this tool and added new functionality compared to > samtools 0.1.19), see: > > https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq > https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq > https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
Going off topic, but I just hit a problem here: https://github.com/samtools/samtools/issues/313 Depending on if the reads have a QUAL value or not, samtool bam2fq will produce either FASTA or FASTQ output - and will happily give a mixture in one file. I know Heng Li has a parser that will take this kind of input, but Galaxy likes to have well defined file formats. I may have to "fix" samtools, perhaps by adding a strict FASTQ output mode? Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
