Use RAPSearch2 with paired end reads

[domenico-simone]

Hi,

I am trying to use the tool with PE reads but I couldn't find how to. From this document http://www.cs.indiana.edu/pub/techreports/TR709.pdf I see there is a -coption which is not present in the command line options (running rapsearch without options) and is not recognized by the tool. I also tried to run with -q with the two PE files as arguments, but apparently only the first one was recognized.

Thanks for your help
Domenico