I ran Bowtie2, mapping my MiSeq reads against a plasmid (8kb) I had to find out if there was any matches. Instead of the usual % matches, the output I got was:
Settings: Output files: "genome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default
I had to change the reference genome to 'one from history' and selected the plasmid sequence.
Am I doing this right? How do I open this file?