lecture_notes:04-09-2010
Differences
This shows you the differences between two versions of the page.
| Next revision | Previous revision Next revision Both sides next revision | ||
|
lecture_notes:04-09-2010 [2010/04/09 22:31] cbrumbau created |
lecture_notes:04-09-2010 [2010/04/11 21:57] learithe |
||
|---|---|---|---|
| Line 9: | Line 9: | ||
| Next week will have a reference genome (POG) to use for testing the tools on. | Next week will have a reference genome (POG) to use for testing the tools on. | ||
| For the most part POG is done; however, there are still some uncertainty with 8 SNPs left. It is definitely past the MIAMI standard at this point. | For the most part POG is done; however, there are still some uncertainty with 8 SNPs left. It is definitely past the MIAMI standard at this point. | ||
| + | |||
| + | Note about sequencing platform quality scores: most platforms are trying to use the phred quality score((http://en.wikipedia.org/wiki/Phred_quality_score)), so the quality score is comparable between the platforms and runs | ||
| + | |||
| + | It can be informative, once reads are mapped, to look at the quality scores for reads with observed errors. | ||
| + | |||
| + | //Pog// assembly is down to only 8 snps & one potentially variable insert | ||
| ===== Main lecture: Assembler graphs ===== | ===== Main lecture: Assembler graphs ===== | ||
| Line 18: | Line 24: | ||
| Differences are "What are the nodes?" | Differences are "What are the nodes?" | ||
| * Overlap: reads | * Overlap: reads | ||
| - | * de Bruijn: k-mers (usually fixed k, k <= length(read)) | + | * de Bruijn: k-mers (usually fixed k, k < = length(read)) |
| === Overlap graphs === | === Overlap graphs === | ||
| Line 37: | Line 43: | ||
| * <- <- (B -> A) | * <- <- (B -> A) | ||
| * 3 different edge types: | * 3 different edge types: | ||
| - | * A to B | + | * same dir: A to B / B to A |
| - | * B to A | + | * tail-to-tail: A' to B |
| - | * A' to B / A to B' | + | * head-to-head: A to B' |
| Need to have some tolerance for error because the reads are noisy. | Need to have some tolerance for error because the reads are noisy. | ||
lecture_notes/04-09-2010.txt · Last modified: 2010/04/12 21:37 by cbrumbau
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
