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Old 04-04-2012, 03:24 AM   #7
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Originally Posted by oxydeepu View Post
tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &
Aside from using a newer version, you might try "tophat -o tophat_new -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq" instead. Depending on how tophat parses how it's called, what you wrote as a command could cause an issue (the error suggests that it's trying to open a file called "-o", suggesting that it's not seeing that as an option but a file name).
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