Tuesday, 27 November 2012

Using samtools to manipulate SAM and BAM files

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I've been using samtools to manipulate bam and sam files during the last few days, and decided to write a few notes so that I won't...
Tuesday, 20 November 2012

How to profile your perl script using nytprof

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To figure out which part of your perl script is taking most of the time, you can "profile" your script. I recently came across a...
Thursday, 15 November 2012

Running GeneWise with HMMs #2

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In a previous post about GeneWise , I talked about how to run GeneWise using HMMs of gene families, for example, HMMs of animal gene familie...
Tuesday, 13 November 2012

Using the geometric distribution in R for bioinformatics

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A geometric distribution G ( p ) with parameter p provides a probability model for the number of trials up to and including the first succ...
Monday, 12 November 2012

Using the binomial distribution in R for bioinformatics

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The binomial distribution B ( n , p ) provides a probability model for the total number of successes in a sequence of n independent trials,...
Friday, 9 November 2012

Getting alignments for all animal gene families from the TreeFam database

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The TreeFam database includes multiple alignments (and phylogenetic trees based on those alignments) for all animal gene families, which is...

Estimating the mean insert size in a BAM file

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If you have a very large BAM file of read-pairs mapped to a genome, it can often be interesting to have an estimate of the mean insert size ...