lecture_notes:05-16-2011
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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? | ||
| Line 6: | Line 13: | ||
| 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). | ||
| Line 18: | Line 19: | ||
| * 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( | ||
lecture_notes/05-16-2011.txt ยท Last modified: 2011/06/13 00:40 by karplus
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