Understanding GSNAP output

[burt]

Hi,

I'm trying out GSNAP as part of the analysis to look for fusion genes and novel transcripts.

I've ran GSNAP with and without the -N parameter. My question is surrounding the output of GSNAP. Without the -N parameters, GSNAP would report all reads and their alignment information rite? How about with the -N parameter enabled? What does GSNAP report? Does it only report the reads that map to possible splice sites? Or does it report all reads as similar to running it without the -N parameter, with additional information for reads that map to possible splice sites?

thanks for reading
-burt