|
|
| Line 3: |
Line 3: |
| == Objectives == | | == Objectives == |
|
| |
|
| === Sept. 2nd 2011 ===
| |
| Overall goals:
| |
| # ID functional polymorphisms with low false negative rate and low false positive rate
| |
| # Support upcoming KJS metabolism paper using strains 2 and 4
| |
|
| |
|
| Becky:
| | ==Notes== |
| # Budget for more sequencing
| | Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US |
| # Number of new strains to sequence
| |
| # Gene list organized by operon/pathway section for upcoming paper
| |
| '''From Becky'''
| |
| Ajs 204: a GntR-type regulator; snp changing R to W in KSJ4
| |
| Ajs 205: a sigma 54; snp changing A to T in KSJ2
| |
| Ajs 205: a sigma 54; deletion frameshift in KSJ4
| |
|
| |
| And I assume the deletion in the string of Gs in Ajs 205 in KSJ4 may be a sequencing error.
| |
| Am I missing anything? If that's it, I guess that would be a pretty easy line in the paper...
| |
| | |
| # Validated polymorphisms from (3) in KSJ2 and KSJ4 (unless those are in a previous email)
| |
| | |
| Eric:
| |
| # Fold-coverage of prior strain sequencing
| |
| ##Is more coverage/different technology going to help reduce false positive rate?
| |
| ## single strain unique polymorphism tables
| |
| ## Focus on gene list provided in Becky(3)
| |
| ## Check polymorphisms provided in Becky(4)
| |
| # New sequencing:
| |
| ## Which technology will be appropriate for upping coverage
| |
| ## Which technology will be most cost-effective for sequencing new strains
| |
| ## For different sequencing center tech:
| |
| ### Cost (consider that prior KJS strain libraries are prepped for 454)
| |
| ### Amount of data
| |
| ### Lengh of reads
| |
| ### wait-time for sequences
| |