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
>> 
>> 
>> 
>> 
>> 
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