Banana Slug Genomics

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lecture_notes:05-16-2011

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 lecture_notes:05-16-2011 [2011/05/16 15:25]eyliaw lecture_notes:05-16-2011 [2011/05/16 15:42]eyliaw Both sides previous revision Previous revision 2011/06/12 17:40 karplus Added "lecture notes" to title.2011/05/16 15:42 eyliaw 2011/05/16 15:42 eyliaw 2011/05/16 15:28 eyliaw 2011/05/16 15:28 eyliaw 2011/05/16 15:27 eyliaw 2011/05/16 15:25 eyliaw 2011/05/16 14:45 eyliaw created Next revision Previous revision 2011/06/12 17:40 karplus Added "lecture notes" to title.2011/05/16 15:42 eyliaw 2011/05/16 15:42 eyliaw 2011/05/16 15:28 eyliaw 2011/05/16 15:28 eyliaw 2011/05/16 15:27 eyliaw 2011/05/16 15:25 eyliaw 2011/05/16 14:45 eyliaw created Last revision Both sides next revision Line 1: Line 1: ====== 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 7: Line 14: = -10 * log_10(1-P(Y=x|Xi=x)) = -10 * log_10(1-P(Y=x|Xi=x)) - Phred: + Quality of our base call based on an alignment: ​ Q1 (quality of read 1), Q2 (quality of read 2), Qa (alignment quality). - 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). + 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?