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-...
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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:

Funding versus Science

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Yesterday, I ended up doing none of the things I intended to do, but cleaned them instead: (1) No bench-work, but a clean bench (and fridge...
Wednesday, November 4, 2009

Decompression

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Whew! Rosie and I just made what I consider a heroic effort to produce a grant application to Genome BC to use DNA sequencing to measure r...
Tuesday, October 27, 2009

Sets of Snps

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So I’ve got pure DNA from my transformants, pretty much ready to send off for our first Illumina runs. I’m just doing a few simple checks w...
1 comment:
Friday, October 23, 2009

Transformants Produced!

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I'll set aside the hack bioinformatics posts for now and give an update on my transformation experiments... We’ve gotten access to a fe...
Thursday, October 15, 2009

Computing Bootcamp

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Whew, I’ve really fallen behind on my blogging... Last week, a good friend of mine came into town for a “northern retreat”, in which he hop...
1 comment:
Thursday, October 1, 2009

Corrected Logos

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Yesterday, I attempted to make some logos out of the degenerate USS simulated data that Rosie sent me. Turns out, I was doing it wrong. Af...
1 comment:
Wednesday, September 30, 2009

Struggling with the Background

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Previously , I had shown some preliminary analysis of Rosie’s simulated uptake data of chromosomal DNA fragments. Rosie also sent me simula...
1 comment: