Bowtie2 reporting alignments count

Question

[bbb]

I am using bowtie2 for mapping genome to reference fasta. As said in bowtie2 manual it reports only the best one alignment. What if read has two best alignments with the same score? Will it report only one random read?

Answer 1

[Thibault D.]

Hi,

Yes, bowtie2 will report a random position for a read (among the best positions) if there are more available position than the requested number. You can modify the maximum amount of position per read. Have a look over here :)