Currently I performed the alignment for DNA-seq data using Bowtie2 using hg19 as reference genome and below is what the alignment shows.
192316851 reads; of these: 192316851 (100.00%) were unpaired; of these: 5956226 (3.10%) aligned 0 times 132246040 (68.76%) aligned exactly 1 time 54114585 (28.14%) aligned >1 times 96.90% overall alignment rate
My question is are those reads aligned > 1 times should be excluded? What does > 1 time alignment stands for in sequencing? Are the alignment score obtained goo enough to be processed further. Looking ahead for response.
Thank you so much.