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Find all significant local alignments between reads
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"confirmed" vs. "seed" hits #48

Closed pb-cdunn closed 7 years ago

pb-cdunn commented 8 years ago

Dr. Myers, I'm having trouble answering this question, so I hope you have time to explain this.

How can "confirmed hits" be greater than "seed hits"?

thegenemyers commented 8 years ago

Seed hits is the number of diagonal bands that meet the seed criterion. Sometimes there can be two or three disjoint alignments found therein because of the low-quality drop outs in pacbio reads. That is there is one hit between two reads A and B, but because of the low quality regions of A and B, daligner finds two or three good locally alignment segments between A and B.

Moreover, confirmed hits is the total number of alignments found, so it is generally twice the number as both A->B and B->A are reported. Maybe this should be fixed to be half as much again.

-- Gene

On 8/26/16, 11:46 PM, Christopher Dunn wrote:

Dr. Myers, I'm having trouble answering this question, so I hope you have time to explain this.

How can "confirmed hits" be greater than "seed hits"?

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