Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only align single end reads. I aligned the two files separately and got results. But I don't know exactly how to deal with those results of BLAST. 1. Should I include the paired reads from two files or include all the reads as results? 2. How to merge the results with the sam file? Because I want to do assembly next step, I want to merge the blast results with gsnap results. Any comments would be appreciated. Thanks.