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--- lecture_notes:05-16-2011 [2011/05/16 21:45]
eyliaw created
+++ lecture_notes:05-16-2011 [2011/06/13 00:40] (current)
karplus Added "lecture notes" to title.
@@ Line 1: / Line 1: @@
-====== Seqprep ======
+====== Seqprep lecture notes ======
+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?
@@ Line 7: / Line 14: @@
     = -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).
--> 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.
-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:
   * Bases 1 and 2 agree: Q1 + Q2
   * Bases 1 and 2 disagree: Q1 - Q2?
-     * (1 - P1)(2/3(

Banana Slug Genomics