Hi, I have been trying to align a specific library, and I used both Bowtie2 and BWA. BWA gives much higher alignment rates, and I am wondering if it is due to bad parameters on my side, bad bowtie version, or something else.
I am running local alignment: bowtie2 -x ref --local -L 6 -p 4 -1 r1.fq -2 r2.fq > out.sam and then tried global alignment
BWA mem ref r1.fq r2.fq > out.sam
Does anyone have an idea? Thanks,