Tophat segment length setting

[wisense]

Hi, all
I use tophat to align my RNA-seq reads to genome. By default, the segment length is 25, and my RNA-seq read length is 101bp, so Tophat will cut the unmapped reads into 4 segments and then mapped them indipendently, does this make sense? For long reads, should I better set the --segment-length parameter to about half of the read length?

Hope to receive your reply
yours
wisense

[jp.]

I have the same problem, can you get me an idea ?

http://seqanswers.com/forums/showthread.php?p=112098#post112098

thank you

Hi, all
I use tophat to align my RNA-seq reads to genome. By default, the segment length is 25, and my RNA-seq read length is 101bp, so Tophat will cut the unmapped reads into 4 segments and then mapped them indipendently, does this make sense? For long reads, should I better set the --segment-length parameter to about half of the read length?

Hope to receive your reply
yours
wisense