Hi David, -1 on the composite datatype for star reference genomes idea Let's use the existing reference genome and index file infrastructure - star is not sufficiently different from bwa or bowtie to warrant anything different IMHO - it works for us but generating the index files manually is a pain - best to write a data manager.
Ross Lazarus Head, Computational Biology, Baker IDI, Melbourne, Australia Pubs: http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ On Thu, Sep 25, 2014 at 6:39 AM, David Hoover <hoove...@helix.nih.gov> wrote: > Why didn't I see these before? Hmm, I thought I had searched both > toolsheds... > > I was kind of hoping someone had tackled this in a different way. It > would be nice if there was a composite datatype for the reference genome. > It is important for users to generate their own personal genome references, > rather than rely on shared, admin-installed indices. And you're correct, > we'd need at least 5-10 separate genome references for each organism, > depending on read length and annotation GTF. > > Back to wheel reinvention. > > BTW, can you tell me which standardly installed tools use composite > datatypes? It's always easier to build thing from comparison, rather than > from scratch. > > David > > -------------------- > David Hoover, PhD > Helix Systems Staff > > On Sep 24, 2014, at 4:14 PM, Björn Grüning <bjoern.gruen...@gmail.com> > wrote: > > > Hi David, > > > > yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I > think Ross has done some work on it. > > The main problem with Star is that is needs special indices (and a lot > of it) and it would be great to offer data managers for it. > > > > Cheers, > > Bjoern > > > > Am 24.09.2014 um 22:05 schrieb David Hoover: > >> Hi, > >> > >> I am developing a tool for STAR (https://code.google.com/p/rna-star/), > and I realize I may be reinventing another wheel. Has anyone else created > a tool for STAR? There's nothing else in the toolsheds for it yet. > >> > >> David > >> > >> -------------------- > >> David Hoover, PhD > >> Helix Systems Staff > >> SCB/DCSS/CIT/NIH > >> 301-435-2986 > >> http://helix.nih.gov > >> > >> > >> > >> > >> > >> ___________________________________________________________ > >> 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/ > >> > > > ___________________________________________________________ > 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/ >
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