User Tools

Site Tools


lecture_notes:05-16-2011

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
lecture_notes:05-16-2011 [2011/05/16 15:42]
eyliaw
lecture_notes:05-16-2011 [2011/06/12 17:40]
karplus Added "lecture notes" to title.
Line 1: Line 1:
-====== 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)
Line 14: Line 14:
     = -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).+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?
lecture_notes/05-16-2011.txt ยท Last modified: 2011/06/12 17:40 by karplus