I have RNA-seq data (PE 2x300) for non-model organisms. I want of aligning them against the assembled genome using BLAT for the identification of introns. Since BLAT can not align paired-end reads. I want to convert them into single-end reads by merging the overlapping R1 and R2.
I would like to know if it makes sense to merge R1 and R2 into one read (if overlaps) or maybe I should work with R1 and R2 separately.
My Best Regards, Prasoon