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 <hooverdm@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.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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