How To Find Repeats And Their Locations
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8.8 years ago
roll ▴ 330

Regarding the repeats, I am interested in finding short reads that had been mapped to more than one distinct positions on the genome. And also which locations has it been mapped to. Is there a tool that already does this? Thanks

duplicates mapping repeats • 1.9k views
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8.8 years ago
cts ★ 1.7k

Some short read aligners will output multiple mapping locations rather than just the best hit. Bowtie 2 will report all alignments of a read with the -a option set. You could look at RazerS 3, which reports all alignments; the paper also has a comparison to other read mappers that can produce multiple alignments.

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