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 <[email protected]> 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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