TopHAT

[bogdan]

Dear all,

I am running TopHat on single read RNA-seq data. It asks for -r option,
although the library is single read. Is there any way to set it up for single reads ?

thanks,

bogdan

[mgogol]

Did you read the manual?

http://tophat.cbcb.umd.edu/manual.html

You can run it with single-end, you don't have to have the -r parameter.