Bowtie:2paired reads mapped to differ contig?

2011-06-06
2013-06-05
  • Hi, I am trying to use Bowtie to map Illumina paired end reads to my assembly contigs and I'd like to know if Bowtie will ever report a case in which one read (first read) is mapped to one contig and its mate (second read) mapped to a different contig.
    Thanks a lot