Tuesday, March 16, 2010

Chromosome "Position Effect"

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I got some data for the transformation frequency at five different markers. They varied. This isn’t anything ground-breaking; reports of ...
2 comments:
Sunday, March 14, 2010

Repression of competence induction by purines

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My illustrious colleagues have been re-examining some of the lab’s old data regarding the repression of competence by purines. The work has...
Thursday, March 11, 2010

What have I got?

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Okay, grant planning part 2... Below is a dense description of the preliminary data I have/will have for writing this next grant... PRELIMI...
2 comments:
Tuesday, March 9, 2010

Another day, another attempt to get a dollar

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Sigh... another grant due soon; this time, it's my last attempt to get an NIH postdoctoral fellowship. My last reviews mainly took iss...
Friday, March 5, 2010

Multiplexing sans barcodes

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Previously, I’d said I wanted to go over how we might obtain many recombinant genotypes by deep sequencing pools of recombinants, since our ...
Friday, February 5, 2010

grantgrantgrant

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Whew! So another grant out-of-the way for now; another one almost done; and my own postdoc re-application in the works… A brief respite… ...
Thursday, January 7, 2010

Using IGV to look at Illumina data

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Out with the oughts in with the tens... Out with Maq , in with BWA ! Recap: I got a bunch of Illumina GA2 data from 5 DNA samples : Our r...
5 comments:
Monday, December 28, 2009

Vacation Post: Uncoiled!

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Number 6... ...in the "Top 10 New Species of 2009" Number 10 is pretty mind-boggling...
Friday, December 11, 2009

Update on problems with analysis

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Ugh. Too much to blog about. The pace of computer work is totally different than with lab work (though in the end they seem equally labor-...
2 comments:
Wednesday, December 2, 2009

Mutagenic recombination?

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Okay, this is pretty cool. I will probably discover that it’s just some artifact of the mapping, but digging into the transformant data som...
1 comment:
Monday, November 30, 2009

Recombinant Genomes: First Pass

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We’ve now got deep sequencing data of donor, recipient, and transformant genomes. And it is, indeed, “deep”, at least in quantity. Here’s ...
2 comments:
Tuesday, November 24, 2009

Incoming Data Deluge

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I am waiting with anticipation... I am about to be drowning in data... >64 million quality filtered paired-end sequencing reads, consti...
Friday, November 20, 2009

Recalculating

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On Wednesday, I put up some tables of data with bad calculations of molecules per cell. Rosie's concerns about the data were misplaced;...
Thursday, November 19, 2009

Bacterial Genome Sequence Links

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I keep meaning to put up these links, so I can find them in the future. They get you to NCBI's genome FTP site. If you click on the ge...
Wednesday, November 18, 2009

Saturation and Chaser

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EDITED: Used bad mol per cell calculation earlier. How much DNA does an average cell in a competent culture take up? I did two experiments...
2 comments:
Tuesday, November 17, 2009

USS uptake with Illumina adaptors

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(I'm somehow deeply amused by the above image. I think it has something to do with the arrow going from the DNA molecule to the sun.) I...

Missing Posts

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Whew! I keep falling behind on my blogging.... Here are the posts that I haven’t written: Using R: (1) Simulation of degenerate USS experim...
Friday, November 6, 2009

Weening myself off of Excel

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In some sense, the computing I did today isn’t really useful, since I already worked out these things using Microsoft Excel. But I’ve been ...
2 comments: