This shows you the differences between two versions of the page.
Both sides previous revision Previous revision | Next revision Both sides next revision | ||
lecture_notes:04-09-2010 [2010/04/11 22:19] learithe |
lecture_notes:04-09-2010 [2010/04/11 22:28] learithe |
||
---|---|---|---|
Line 103: | Line 103: | ||
Realistically, there are issues: | Realistically, there are issues: | ||
+ | == End of Contig boundaries: == | ||
- | End of Contig boundaries: | ||
what if A->B and A->C and A->D BUT A->B and A->C are inconsistent with each other? | 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 | … 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 | also end of contig if there are no more edges from the node | ||
- | Spurs: | + | == Spurs: == |
<code> | <code> | ||
kmer -> kmer -> kmer -> kmer -> kmer | kmer -> kmer -> kmer -> kmer -> kmer | ||
Line 116: | Line 116: | ||
path diverges but does not reconverge, resulting in source/sink dead-ends (these are likely due to read errors) | path diverges but does not reconverge, resulting in source/sink dead-ends (these are likely due to read errors) | ||
- | Bubbles: | + | == Bubbles: == |
<code> | <code> | ||
/-> kmer -> kmer -> kmer -\ | /-> kmer -> kmer -> kmer -\ | ||
Line 124: | Line 124: | ||
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 | 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 | ||
- | Other issues: | + | == 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 | + | 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 |
- | Multiple paths: | + | == Multiple paths: == |
<code> | <code> | ||
A B | A B | ||
Line 147: | Line 145: | ||
Largest bias usually comes from PCR for amplification. | Largest bias usually comes from PCR for amplification. | ||
- | + | ===Assembly:=== | |
- | Assembly: | + | algorithms (both overlap and de Bruijn) need to collapse bubbles and trim spurs.\\ |
- | algorithms (both overlap and de Bruijn) need to collapse bubbles and trim spurs. | + | spurs: discard if their read count is low\\ |
- | spurs: discard if their read count is low | + | |
bubbles: tricky, because they can represent real, divergent paths | bubbles: tricky, because they can represent real, divergent paths | ||
- | |||
- | |||