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Old 04-13-2011, 07:02 AM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default tophat - r option - single end reads


I have GAII data - 36 bp single end reads.

I am using tophat following option

tophat -p 14 btie/indexes/hg18 sample1.fastq -o awb --segment-mismatches 3

Error: you must set the mean inner distance between mates with -r

I get the error forcing me to set -r option. These reads are single-end reads, why tophat wants me to set -r.

can I instead set -r 0?
any help appreciated.

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Old 05-26-2011, 09:23 PM   #2
Location: Madison, WI

Join Date: May 2011
Posts: 10
Default Same Issue

I am trying to map 42 bp single reads and have the same error message.
kreitinger is offline   Reply With Quote
Old 05-28-2011, 06:33 PM   #3
Senior Member
Location: East Coast, US

Join Date: Jun 2010
Posts: 177


Please check if you are using the latest version of tophat. I did one project 2 months ago using Tophat on single-fragment reads and it worked. My actual command was

tophat -p 6 --allow-indels -o $id $ref $id.fq

Hope it helps.

DZhang is offline   Reply With Quote
Old 06-07-2011, 08:25 AM   #4
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Location: Germany

Join Date: Jun 2011
Posts: 9

For SOLiD reads, you have to put the -Q option in the list of options, and specify the _QV.qual file at the end after the reads file, like so:

tophat -C -Q -G reference.gtf reads_filename.csfasta reads_filename_QV.qual
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