SHRIMP opp-in for SOLID PE??

[SMHfrog]

I've been using SHRiMP to map reads to a genome. I now have paired-end reads. My understanding is that SOLiD paired-end reads are colinear (same strand) and backward (the sequences point inwards towards each other).

If I'm understanding this right, this isn't an option in SHRiMP. The closest, and what people appear to be using, is "opp-in": opposite strands, backwards.

Does this setting work? Or am I completely mis-interpreting something?

Thank you!

[jmandel]

I'm actually having exactly the same problem. Do you or anyone here have new insights on the choice of the paired-end mode in SHRiMP for paired-end SOLID data ?

Jonas

[vitorpiro]

I use SHRiMP for SOLID mate-paired data. The option that works in pair mode is: "col-fw" (colinear, second is forward).