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2 hours ago by

Hello everyone

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.

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