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Old 02-07-2011, 08:04 AM   #1
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Location: Boston

Join Date: Jul 2010
Posts: 7
Default Cufflinks crashes on BAM output from TopHat


I am trying to run Cufflinks (version 0.9.3) on BAM output from TopHat (1.1.1). Unfortunately it crashes in the middle of running. In most cases it stops at inspecting reads step at around 40%. Here is the command I used to run Cufflinks.

cufflinks -L hg19_cuff -p 6 -r /bowtie-0.12.7/indexes/hg19.fa accepted_hits.bam

It crashes even when I ran it on a much smaller dataset but not all the time. It's a 90 bp paired end dataset with total around 49 million alignment output from TopHat.

I have read from the Cufflinks website that the new 0.9.3 version has fixed the crash bug. Any help will be much appreciated,

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