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Old 02-16-2011, 12:02 AM   #3
Location: Sweden

Join Date: Nov 2009
Posts: 12
Smile Problem solved

Hello, thank you!
It really worked with 8 threads. First problem was, that I ran 16 treads of tophat on 8 cores and they tried to read to the same folder.
Second problem, as appeared later, was the empty reference file. They say at tophat manual, that reference.fa will be built automatically with the first run of tophat. Nut I built in manually using bowtie-inspect. Now tophat produces junction database!
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