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lecture_notes:05-16-2011 [2011/05/16 21:45] eyliaw created |
lecture_notes:05-16-2011 [2011/05/16 22:28] eyliaw |
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====== Seqprep ====== | ====== Seqprep ====== | ||
+ | Phred: | ||
+ | * 66 -> 0 (33) (Or not... makes sense to not have 0) | ||
+ | * 33 - 64 = -31 in most cases | ||
+ | |||
+ | Systematic base-calling biases in Illumina exist. I.e. read one thing going one way, something else going the other. | ||
+ | |||
+ | |||
How does Seqprep do error correction? | How does Seqprep do error correction? | ||
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Given that base Xi is x: | Given that base Xi is x: | ||
= -10 * log_10(1-P(Y=x|Xi=x)) | = -10 * log_10(1-P(Y=x|Xi=x)) | ||
- | |||
- | Phred: | ||
- | 66 -> 0 (33) | ||
- | 33 - 64 = -31 in most cases | ||
- | |||
- | Systematic base-calling biases in Illumina exist. I.e. read one thing going one way, something else going the other. | ||
Quality of an alignment: Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality: agree and disagree). | Quality of an alignment: Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality: agree and disagree). | ||
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* Bases 1 and 2 agree: Q1 + Q2 | * Bases 1 and 2 agree: Q1 + Q2 | ||
* Bases 1 and 2 disagree: Q1 - Q2? | * Bases 1 and 2 disagree: Q1 - Q2? | ||
- | * (1 - P1)(2/3( |