Getting started with Picard

Updated hyperlinks on the 2015 January 26th; please comment if you find any more dead links. Picard is a suite of Java-based command-line utilities that manipulate SAM/BAM files. Currently, I'm analysing some paired-end libraries and I wanted to calculate the average insert size based on the alignments; that's how I found Picard. While reading the...

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Getting started with paired-end reads

I've wanted to write this post for a while, but I never had to work with paired-end libraries, so the impetus wasn't quite there. Finally I've decided to take a look at some paired-end libraries at work and as usual, I will test some simple examples before I touch the real data. For those not...

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Quantile normalisation in R

Updated 2015 January 14th to include a slide from Rafael. From Wikipedia: In statistics, quantile normalization is a technique for making two distributions identical in statistical properties. To quantile normalize two or more distributions to each other, without a reference distribution, sort as before, then set to the average (usually, arithmetical mean) of the distributions....

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