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Question: Minimum Length Of Read Segments
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gravatar for Du, Jianguang
6.3 years ago by
Du, Jianguang • 380
Du, Jianguang • 380 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
rna-seq tophat • 2.7k views
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Du, Jianguang • 380
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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