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Old 09-23-2011, 12:11 PM   #1
Location: US

Join Date: Mar 2010
Posts: 25
Default Tophat command for single end reads

Hi Everyone,

I'm trying to run tophat on single end illumina reads..but end up getting error message telling me to input the distance between the 2 reads (r). Has anyone run tophat on single runs? What is the command for it?

Some one had posted similar question in the past..but that has not yielded into the command.

Thanks a lot!!

Kaustubh Gokhale.
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Old 09-24-2011, 02:30 AM   #2
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

It's worked for me with single-end reads. If it's producing errors about read-pair distance, the input is probably specified incorrectly. Just make sure you split the file names by commas instead of spaces. There's an additional option (--segment-length) for splitting shorter reads by adjusting the segment size (this is warned about in the tophat output when it detects short reads).

tophat  bwtindex lane1reads.fastq,lane2reads.fastq,...,laneNreads.fastq
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