Hi, I am using bowtie for the alignment and find that for the reads with multiple hits, the first alignment is more likely (but not always) to be the correct alignment even if the mismatching information is the same.
So I wonder how does bowtie order the multiple hits (if there are) of a specific read?
Do they have some scheme to search the more probable locations first?
So I wonder how does bowtie order the multiple hits (if there are) of a specific read?
Do they have some scheme to search the more probable locations first?