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: