lecture_notes:05-16-2011
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A PCRE internal error occured. This might be caused by a faulty plugin
====== 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? Quality scores Q_i = -10 * log_10(P(i is wrong)) Given that base Xi is x: = -10 * log_10(1-P(Y=x|Xi=x)) 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: * Bases 1 and 2 agree: Q1 + Q2 * Bases 1 and 2 disagree: Q1 - Q2?
lecture_notes/05-16-2011.1305585769.txt.gz · Last modified: 2011/05/16 22:42 by eyliaw
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Discussion
The notes here are so terse as to be incomprehensible.