Hello all, Further to recent discussions about dealing with large FASTQ files, and the short term advantages of gzipped FASTQ as a filetype in Galaxy (or gzipped files in general, https://bitbucket.org/galaxy/galaxy-central/issue/666/ ), we also discussed the merits of unaligned BAM files.
It occurred to me this could be defined in Galaxy as subclass of the existing BAM definition, with a simple sniffer based on running "samtools idxstats" to find out if there are any mapped reads or not. This would then make it easy for tools capable of aligning SAM/BAM to list unaligned-bam as a Galaxy input format (avoiding complications of realigning previously aligned reads). You could also have a matching aligned BAM subclass, then tools like SNP detectors should insist on an aligned BAM file for input. Does this sound reasonable? 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/