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/

Reply via email to