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 15:25]
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: 
 +  * 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?
lecture_notes/05-16-2011.txt · Last modified: 2011/06/12 17:40 by karplus