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lecture_notes:05-16-2011 [2011/05/16 22:28] eyliaw |
lecture_notes:05-16-2011 [2011/06/13 00:40] (current) karplus Added "lecture notes" to title. |
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- | ====== Seqprep ====== | + | ====== Seqprep lecture notes ====== |
Phred: | Phred: | ||
- | 66 -> 0 (33) (Or not... makes sense to not have 0) | + | * 66 -> 0 (33) (Or not... makes sense to not have 0) |
- | 33 - 64 = -31 in most cases | + | * 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. | Systematic base-calling biases in Illumina exist. I.e. read one thing going one way, something else going the other. | ||
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= -10 * log_10(1-P(Y=x|Xi=x)) | = -10 * log_10(1-P(Y=x|Xi=x)) | ||
- | Quality of an alignment: Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality: agree and disagree). | + | Quality of our base call based on an alignment: Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality). |
If we assume that the alignment is perfect: | If we assume that the alignment is perfect: | ||
* 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? |