Hi, Am 24.09.2014 um 22:39 schrieb David Hoover:
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.
Yes :( For me this was to cumbersome and I decided to wait until the TopHat successor will be released :)
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.
Sure. Have a look at the Galaxy wrappers from Peter: https://github.com/peterjc/galaxy_blast Galaxy Datatypes are composite. Cheers, Bjoern
David
-------------------- David Hoover, PhD Helix Systems Staff
On Sep 24, 2014, at 4:14 PM, Björn Grüning <bjoern.gruening@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
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