Genomics palindromes

Leonor
2012-07-25
2013-06-05
  • Leonor
    Leonor
    2012-07-25

    How does Bowtie deal with genomic palindromes if I indicate the -m 1 option? If I have one read that aligns in a palindromic region of the genome, then the read can be aligned in both + and - strands. Are this two alignments taken as a unique alignment or are they two distinct alignments?

    Thank you in advance,
    Leonor