This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
lecture_notes:05-16-2011 [2011/05/16 22:25] eyliaw |
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? | 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? |