Computational biology and genomics
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…
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…
Updated 2019 October 11th to explain the index_to_mean function. 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. So…