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Back to crunching personal genomic data

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I&# Read more...

Posted
November 22nd, 2012

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Back to crunching personal genomic data

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I&# Read more...

Posted
November 22nd, 2012

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Back to crunching personal genomic data

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I&# Read more...

Posted
November 22nd, 2012

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GEDmatch needs funds!

I noticed today that GEDmatch is trying to raise funds to cover the cost of their web services. What are those services? Basically if you get raw data back from direct-to-consumer genotyping firms GEDmatch allows you to run further analytics. You can do some of these yourself…but most people aren’t going to know how to convert their files into pedigree format and use PLINK. As genotype data becomes more and more common there’ll Read more...

Posted
October 22nd, 2012

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Neandertal one stop shopping

If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It’s a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the signals of admixture in non-Africans being genuinely Neandertal seem to be increasing as we progress. In other words, you should weight the “o Read more...

Posted
October 17th, 2012

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Dienekes and ADMIXTOOLS

Less than a month ago I pointed to the release of ADMIXTOOLS. Unfortunately, though I have a desktop at home devoted purely to my personal genomic hobbies I haven’t been able to free up the time on weekends to start doing my own analysis. This is pretty pathetic, and sometimes I get a little depressed at how little usage there is of all the great scientific software released into the public domain. But in case you haven’t seen it, I Read more...

Posted
October 9th, 2012

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Online open human genomic data sets

I had a friend recently email me about human genetic data sets. Some, like POPRES, are restricted to researchers. But there are a lot of data available for the public. Zack Ajmal has posted on most of them at some point. Feel free to post links to others in the comments. Share Source: Discover Magazine – Gene Expression Tags: biotechnology, genomics Read more...

Posted
October 7th, 2012

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What is going on with plant domestication?

PNAS has a paper on barley domestication out right now. It is nicely open access, so read it yourself, and come right back! I have to admit that I did not like the paper too much. It seemed to derive far too many conclusions from a few rudimentary (for today at least) phylogenetic methods. In particular I’m very skeptical of the idea that there are two barely lineages here which diverged ~3 million years B.P. But this isn’t partic Read more...

Posted
October 3rd, 2012

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ADMIXTOOLS is out

The time for commentary uninformed by DIY exploratory analysis is fast coming to a close. The alpha version of ADMIXTOOLS is out. It’s a moderately large download, 166 MB in compressed format. Do note that most of this consists of data files, not the program itself. I uploaded a zip of the README files if you are hesitant. Dienekes has a preview. I probably won’t poking around until this weekend. If you are confused as to why this i Read more...

Posted
September 14th, 2012

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The West Asian mix

IE-speaking West Europeans are West Asian-admixed relative to Non-IE speaking Basques. Dienekes explicitly confirms what seems obvious using ADMIXTURE. When I get a chance I’m going to see if this difference is evident when comparing some South Indian (non-Brahmin samples) I have against Gujaratis. For what it’s worth I am told that ADMIXTOOLS will be out this week. Share Read more...

Posted
September 10th, 2012

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