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lecture_notes:04-09-2010 [2010/04/11 22:09] learithe |
lecture_notes:04-09-2010 [2010/04/11 22:28] learithe |
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Realistically, there are issues: | Realistically, there are issues: | ||
+ | == End of Contig boundaries: == | ||
- | Spurs: | + | what if A->B and A->C and A->D BUT A->B and A->C are inconsistent with each other? |
+ | … A becomes “end of contig”, because you aren’t sure where to go next | ||
+ | also end of contig if there are no more edges from the node | ||
+ | |||
+ | == Spurs: == | ||
<code> | <code> | ||
kmer -> kmer -> kmer -> kmer -> kmer | kmer -> kmer -> kmer -> kmer -> kmer | ||
\-> kmer -> kmer -> kmer (off to nowhere) | \-> kmer -> kmer -> kmer (off to nowhere) | ||
</code> | </code> | ||
+ | path diverges but does not reconverge, resulting in source/sink dead-ends (these are likely due to read errors) | ||
- | Collapse bubbles: | + | == Bubbles: == |
<code> | <code> | ||
/-> kmer -> kmer -> kmer -\ | /-> kmer -> kmer -> kmer -\ | ||
Line 116: | Line 122: | ||
</code> | </code> | ||
- | Other issues: | + | path splits due to a SNP but then converges. this can happen with real SNPs, read error SNPs, and real repeats which differ by a SNP or two |
- | Loop: | + | == Loop: == |
<code> | <code> | ||
kmer -> kmer -> kmer -> kmer -> kmer -> kmer -> kmer | kmer -> kmer -> kmer -> kmer -> kmer -> kmer -> kmer | ||
\- kmers <-/ | \- kmers <-/ | ||
</code> | </code> | ||
+ | tandem repeats will generate a circle, but have edges in and out; hard to disambiguate copy # though. If the data is really clean (ie, in/out edges are ~10 read-depth with low SD, and inside circle has ~20 read-depth with low SD), can guess that there might be 2 copies of the repeat, but not highly reliable | ||
- | Take the loop? | + | == Multiple paths: == |
- | + | ||
- | Multiple paths: | + | |
<code> | <code> | ||
A B | A B | ||
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Largest bias usually comes from PCR for amplification. | Largest bias usually comes from PCR for amplification. | ||
- | Need to collapse the graph (both overlap and de Bruijn) to assemble the reads. | + | ===Assembly:=== |
+ | algorithms (both overlap and de Bruijn) need to collapse bubbles and trim spurs.\\ | ||
+ | spurs: discard if their read count is low\\ | ||
+ | bubbles: tricky, because they can represent real, divergent paths | ||
+ | |||
+ |