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lecture_notes:05-16-2011

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?

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?

Discussion

, 2011/06/12 17:40

The notes here are so terse as to be incomprehensible.

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lecture_notes/05-16-2011.txt · Last modified: 2011/06/12 17:40 by karplus