I have 150-bp paired-end sequencing reads, and I am mapping them with Bowtie with the following parameters:
bowtie -v 2 -p 16 -m 1 --minins 0 --maxins 1000 --best --allow-contain --solexa-quals
However, I get as output only fragment sizes >150bp. My thinking was that parameter --minins 0 tells Bowtie to accept all small DNA fragments, but apparently it's not?
Could you please advise how to adjust Bowtie parameters to get all the smaller fragments in this mapping?