Ross,
About the index files: It is way easier to have pre-built index files.
However, when running a 2-pass STAR run, a user will need to generate
their own reference index files based on the output SJ.tab.out file
created in the first pass. Is this incorporated into your tool?
About shared memory: I am under the impression that the latest version
of STAR has deprecated this feature. I am unclear how this would help
unless a single large-memory machine was dedicated to running all STAR
jobs. Is this the case?
Also, does the tool merge the SAM/BAM file with the output chimeric SAM
file?
David Hoover
On 9/24/2014 7:03 PM, Ross wrote:
Hi All,
That (fubar in testtoolshed) star wrapper was derived from one
originally written by Jeremy Goecks. I modified it for multiple inputs
and added a few tweaks and it has been in production use in our group
for about 6 months so I'm pretty sure it works reasonably well in our
hands at least.
I would really appreciate any available help getting it to a proven
useful state - suggestions and code welcomed. I have not moved it to
the main toolshed because aside from some encouragement, I've had no
feedback to suggest it's working - or not. It is extremely fast - we
regularly see 200-300M reads per minute in the logs!
We regularly run a whole experiment worth (eg 12 - 24) fastq files
simultaneously with the shared memory option working on our cluster -
see the readme.
Star index files made with a gene model (requires valid gff3) are huge
- 20-30GB for hg19 - hence the need for shared memory if you run
multiple jobs. That will eventually become a serious problem if you
really want to allow users to make their own - we definitely do not.
You need to be very careful about matching the gene model gff3 file to
the reference and I had enough trouble getting it right for the few
major genomes we use to make me think that I do not want users trying
to do that generating 25GB of rubbish every time they get it wrong.
There are challenges to do with needing different indexes for
different length reads but we are seeing fairly consistent 60bp single
ended reads for most of the incoming RNA seq experiments.
A data manager would be a boon if anyone cares to write one...
On Thu, Sep 25, 2014 at 6:55 AM, Curtis Hendrickson (Campus)
<curt...@uab.edu <mailto:curt...@uab.edu>> wrote:
Bjorn
We'd be interested in this tool, as well. Any idea how close to
functional it is?
I see it's only on TEST toolshed, and not on production, at this
point.
I don't see any related Trello card when searching on "star"
Regards,
Curtis
Galaxy Admin @ University of Alabama at Birmingham
-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
<mailto:galaxy-dev-boun...@lists.bx.psu.edu>
[mailto:galaxy-dev-boun...@lists.bx.psu.edu
<mailto:galaxy-dev-boun...@lists.bx.psu.edu>] On Behalf Of Björn
Grüning
Sent: Wednesday, September 24, 2014 3:15 PM
To: galaxy-dev@lists.bx.psu.edu
<mailto:galaxy-dev@lists.bx.psu.edu>; hoove...@helix.nih.gov
<mailto:hoove...@helix.nih.gov> >> David Hoover
Subject: Re: [galaxy-dev] tool for STAR RNA-seq aligner
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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