July 2010
1 post
4 tags
From Tophat to Pysam
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 samtools and tried a conversion.
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April 2010
2 posts
Inferring Heterozygosity from SNP data
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: quantitative comparison to...
5 tags
Why we are "Python Fanboys"
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 too...