Please does anyone have a way to resolve the multiple alignment from bowtie2 to produce alignments with only the best alignment score?
A hit at a locus could be shifted about 1bp with another alignment reported but with a different alignment score. The same hit could be shifted by 6bp with another different alignment score.
This I believe is happening due to the -secondary switch to output secondary alignments. I need the secondary alignments to know where the copies of the reads are. I want only the high quality alignments for a read at a locus without having the ones at locus+N1, locus+N2 etc.
An illustration is shown in the figure below.
The alignment at locus 2 ends at 688, shifting the read by 1 base, there is another alignment with a different alignment score.
I should state that I am aligning to a chromosome with highly repetitive DNA. I am using bowtie2 due to its higher sensitivity.
Any help would be highly appreciated.
Thanks in advance.