There seems to be a distinct alignment format for almost every application out there requiring people to write format converters. Recently, I've seen the majority of tools center around Illumina align format, Eland, GFF, and SAM. There is very little mention of supporting Solid formats, which include GFF and SAM.
The downstream applictions (ChIP-Seq and RNA-Seq) seem to use align or Eland. Unfortunately for me and other Solid users, we need to convert our Solid alignment format to Illumina align. I don't have a problem with this, the conversion should be straight-forward Perl script. My problem though is I don't know the specs for the align format.
Is there a reference for the different file formats, or a tool that performs the conversions for all these different tools? That could be one of the most useful tools available. It seems like 90% of my time is researching how to input my data into the different analysis programs out there.
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