Thread: BFAST published
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Old 11-11-2009, 12:33 PM   #7
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Originally Posted by nilshomer View Post
What panel are you looking at (sensitivity or false mapping)? Obviously the sensitivity cannot be 100% due to the repetitiveness of the human genome. For false-mapping, with no errors I don't see a >0% false mapping rate in Figure 3.
Unless sensitivity is too bad, I do not care too much about false negatives. I am looking at false positives (2nd column). At 0-mismatch/indel, both bwa and bowtie have ~6% error rate while others have 0%.

We don't clip the reads. The "local alignment" we use is a global alignment to a window the candidate location. In other words, we enforce that the entire read must align to some subset of bases in the reference.
This is reassuring. Thanks for the explanation.
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