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From Tophat to Pysam July 21, 2010
I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file. This meant I need to convert filetypes. So, I fired up sa […]
Inferring Heterozygosity from SNP data April 20, 2010
This looks straightforward. n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
Why we are "Python Fanboys" April 15, 2010
I think I can safely say that we’re all Python evangelists. In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is. Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]

Does England Just Need a Good Shag?
Published: June 22, 2010
Source: The New Republic - The Goal Post Feed
Things are not looking good for England. Two draws against opponents many in the global football community had quickly written off. The passes aren’t coming through, the runs are being cut off, the set pieces...
Environmental change enhances cognitive abilities in fish.
Published: April 26, 2010
Source: pubmed: "plos biology"[jour]
My Note: Clearly it's important to eat well.
Environmental change enhances cognitive abilities in fish. PLoS Biol. 2010;8(4):e1000351 Authors: Kotrschal A, Taborsky B Flexible or innovative behavior is advantageous, espe...
Version Control Failure
Published: April 8, 2010
Source: Omics! Omics!
My Note: This is moderately terrifying. Luckily, there is only one anole genome version publicly available at this point in time.
Well, it was inevitable. A huge (and expensive) case of confused human genome versions.While the human genome is 10 years old, that was hardly the final word. Lots of mopping up remained on the original proj...
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