Workflow Wednesdays – Coverage analysis 2. and other alignment statistics

02/10/2013

As I promised last week, I’ll show you some command line based alignment analysis tools this week. As there are basically an endless number of methods for generating alignment statistics, feel free to share additional tips and tricks in the comment section!

Bioinformatics for Beginners – Finding known somatic mutations

30/09/2013

I’ve already written about mutation databases a few weeks back (you can read my post here), but there is a big group of variations I haven’t mentioned in my post. These variants are somatic mutations (if you’re not familiar with the main classes of mutations, check out this page). Very...

Flashcard Fridays – A night at the museum

27/09/2013

If you’ve ever worked as a field biologist, you know how hard sample collection can be. It’s a tough job even if you only want to collect biological samples from a small number of animals living in a relatively confined area (I could tell you long stories about the two...

Workflow Wednesdays – Coverage analysis 1.

25/09/2013

Nowadays, when whole exome and whole genome alignments are becoming fairly routine and even gene panels often target hundreds of genes, it’s no longer a valid option for researchers to visually check the quality of alignments. Generating coverage measures and statistics is a good tool for identifying sequencing or alignment...

Bioinformatics for Beginners – ROSALIND

23/09/2013

The Rosalind project provides an opportunity for learning bioinformatics through problem solving. Rosalind works the following way: you select a problem to solve from a list of available problems, you look through the problem and work out your solution (an example input and output is provided for each problem), you...