Hello Jianguang,
Unless you know that your genome has exons that are shorter in length
than 25 bases long, then it is not necessary to modify this parameter.
http://tophat.cbcb.umd.edu/manual.html
--> How does TopHat find junctions?
If shorter, then set the parameter to be that shortest length. Please
keep in mind that lowering this value makes the job more sensitive at
the cost of making it also more computationally intensive. If the job
becomes too large for the public Main Galaxy instance, a cloud instance
would be an alternative: http://usegalaxy.org/cloud
Best,
Jen
Galaxy team
On 8/16/12 10:44 AM, Du, Jianguang wrote:
Dear All,
I am going to run Tophat with RNA-seq dataset to observe alternative
splicing events. There is a parameter for Tophat: "Minimum length of
read segment". According to "implemented Tophat options", the
description for "Minimum length of read segment" is "Each read is cut up
into segments, each at least this long. These segments are mapped
independently. The default is 25". The length of my reads is 36bps,
should I change this parameter based on the length of my reads? How
long should I input?
Thanks.
Jianguang Du
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
