Coffee bacs: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 9: | Line 9: | ||
CA1A : CA3, genomeLen=100K | CA1A : CA3, genomeLen=100K | ||
CA1B : CA4 | CA1B : CA4 | ||
CA1A: | |||
* The CA_24Sept07 assembly had a 15KB long degenerate. This | |||
degenerate has high coverage (~ twice the average) and high GC% | |||
(41% vs avg of 36%). There are no correlated SNP's in it and no | |||
missoriented mates so it is probably not a collapsed repeat. I | |||
wonder if due to its high GC this area in the BAC might have got | |||
cloned preferentially.The degenerate has several links to placed | |||
contigs. | |||
* A new assembly run by setting the assembly size to 100K managed to | |||
incorporate the previous degenerate into its longest scaffold. | |||
This assembly is located under | |||
/fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/ | |||
* Several scaffolds are linked to other scaffolds by single mate | |||
pair links. CA needs at least 2 mate pairs in order to link | |||
contigs together. | |||
* Bambus, run with redundancy=1 resulted in 10 scaffolds, but not | |||
all are linear . The Bambus files are located under | |||
/fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/bambus/ | |||
* Celera Assembler version 4 (CA4) did not perform any better than | |||
CA3.11 | |||
* autoJoiner did not close any sequence gaps | |||
CA1B: | |||
* The CA4 assembly closed one sequence gap from the CA_24Sept07 | |||
assembly. The CA4 assembly is located under | |||
/fs/szasmg2/coffee/CA1B.inputs/CA_04Oct07-CA4/ | |||
* autoJoiner did not close any sequence gaps |
Latest revision as of 21:37, 15 January 2008
Location:
/fs/szasmg2/coffee/
BACS:
CA1A CA1B
Best assemblies:
CA1A : CA3, genomeLen=100K CA1B : CA4
CA1A:
* The CA_24Sept07 assembly had a 15KB long degenerate. This degenerate has high coverage (~ twice the average) and high GC% (41% vs avg of 36%). There are no correlated SNP's in it and no missoriented mates so it is probably not a collapsed repeat. I wonder if due to its high GC this area in the BAC might have got cloned preferentially.The degenerate has several links to placed contigs. * A new assembly run by setting the assembly size to 100K managed to incorporate the previous degenerate into its longest scaffold. This assembly is located under /fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/ * Several scaffolds are linked to other scaffolds by single mate pair links. CA needs at least 2 mate pairs in order to link contigs together. * Bambus, run with redundancy=1 resulted in 10 scaffolds, but not all are linear . The Bambus files are located under /fs/szasmg2/coffee/CA1A.inputs/CA_04Oct07-CA3-100K/bambus/ * Celera Assembler version 4 (CA4) did not perform any better than CA3.11 * autoJoiner did not close any sequence gaps
CA1B:
* The CA4 assembly closed one sequence gap from the CA_24Sept07 assembly. The CA4 assembly is located under /fs/szasmg2/coffee/CA1B.inputs/CA_04Oct07-CA4/ * autoJoiner did not close any sequence gaps