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Old 10-21-2009, 01:10 AM   #1
Location: Paris

Join Date: Sep 2009
Posts: 14
Default TopHat limit length

Dear all,

I'm trying to use Tophat with 8 million single-end reads of 75 bp. I set all options that concern minimum intron length to 30 (because the minimum intron length in my genome reference is 39), all other option are set to the default value:
-i 30
--min-coverage-intron 30
--min-segment-intron 30
--min-closure-intron 30

In this conditions it works until the step of "Joining segment hits", but it never passed this step. I'm still waiting since yesterday morning!!!!
Is it normal? How many times does it take?

If I test this conditions on 8 millions single-end read of 35bp it completly works in ~25 minutes.

thanks for your help

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Old 10-21-2009, 08:32 AM   #2
Cole Trapnell
Senior Member
Location: Boston, MA

Join Date: Nov 2008
Posts: 212

How are you running the program (i.e. command line options)? Which version are you using?

It's not normal: I routinely run more than 150 million 75bp reads, and that step takes no more than an hour (when our filesystem is running slowly).
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Old 10-21-2009, 11:50 PM   #3
Location: Paris

Join Date: Sep 2009
Posts: 14


I use the last version of bowtie (0.11.3) and the last version of tophat (1.0.11) with the command line:

./tophat-1.0.11/bin/tophat -i 30 --min-coverage-intron 30 --min-segment-intron 30 --min-closure-intron 30 -o res-70/ index/trichoderma-ref 70a.fq

The same commande line works well on the 35bp read.
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