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Old 12-02-2012, 04:41 PM   #1
abh
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Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default Tophat RnaSeq(20-36bp)bp reads

Hi,

I have 2 RnaSeq fq files that i need to analyze.i did the quality trimming and adapter trimming for the files as they were need to do it

then i got 2 output files that are 1.fq file(36 million bp reads) and 2.fq(40 million bp reads) with length of 20-36bp reads in it

I used tophat for aligning them to reference.then when i ran the tophat it is saying to decrease the --segment-length to half of the read length.

do i need to give the --segment-length to 18?or run with the default 25?

i need help in --coverage-search( when i used it in default it was saying that th e tophat will work slow if i used it)do i need to use the --no-coverage-search option for this?does it have any difference?

Please help me i am new in using the tophat

Thank you
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