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



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