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
-Original Message-
From: 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; hoove...@helix.nih.gov David Hoover
Subject: Re: [galaxy-dev] tool for STAR RNA
, 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
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
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
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
-Original Message-
From: 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; hoove...@helix.nih.gov David Hoover
Subject: Re: [galaxy-dev] tool for STAR RNA-seq
] 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
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
