I am using Bowtie2 to align the reads to lambda_virus genome using the following command.
./bowtie2 -x lambda_virus -U example/reads/reads_1.fq -S eg1.sam
It shows following output in the console i.e. 10000 reads; of these: 10000 (100.00%) were unpaired; of these: 596 (5.96%) aligned 0 times 9404 (94.04%) aligned exactly 1 time 0 (0.00%) aligned >1 times 94.04% overall alignment rate
I want to relax the edit distance parameter so that each and every read can get aligned. Can somebody suggest how to do it in bowtie. Also i want the set of reads that get perfectly aligned with 0 edit distance. How to do that in bowtie. I tried reading the manual but it is using all the biological definitions and i am myself from computer science background.
Thanks in advance,