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Old 11-04-2009, 11:08 AM   #1
statsteam
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Location: Californica

Join Date: Sep 2009
Posts: 18
Default TopHat questions

Hi,

I have a few general questions.

I am planning to do the junction mapping using 76bp reads.

What is the good anchor length to use (I am currently using 5 with a -5 option)?
Since the reads are long (I used to use 32 bp reads), I am wondering if I can allow more than 3 matches per segment. TopHat currently allows upto 3 mismatches per segment. I initially wanted to set it up with
--segment-length 76 -- segment-mismatches 4
but TopHat threw an error saying the number of mismatches is upto 3 per segment. So, I am currently using
--segment-length 38 --segment-mismatches 2

Even though my current setting mimics what I wanted to do, it will not be the same as allowing upto 4 mismatches because the 3' end tends to have more sequencing errors.

Thank you,
Statsteam
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Old 11-10-2009, 03:48 AM   #2
colindaven
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Location: Germany

Join Date: Oct 2008
Posts: 415
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Hi Statsteam,

I'm new to Tophat but have used Bowtie extensively, which Tophat uses. There is a limit of three mismatches per seed in Bowtie.

Not sure about your other questions yet.

Hope that helps

Colin
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