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I’m puzzled by executive compensation

I find it easy to understand that Dan Brown makes $22e6 a year: He writes books, people buy them. He gets paid a percentage. I can even understand that Judge Judy makes $47e6 a year: she stars in a TV show that people (effectively) pay to watch. What I can not understand is how an…

From Tony Hall https://www.flickr.com/photos/anotherphotograph/

The utility of wealth

Ubiquitous upward economic mobility is a flawed goal because wealth (and ambition) does not have the same utility for everyone. The New Yorker (where James Thurber got his start) is still one of those places one can go to to think. I was browsing it this morning and found this article titled “The Mobility Myth“.…

Raw (unaligned), paired reads in a BAM file

Since BAM files are the binary version of SAM files, which in turn stand for Sequence Alignment/Mapping, its a little strange to store unaligned data (the raw reads from the sequencer) in a BAM. However, as eloquently argued by others, the text based FASTQ format is showing its age and an indexed binary file is a…

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SAM! BAM! VCF! What?

As part of an exercise I’m doing I was supplied with a FASTQ file which contains a set of reads and I needed to figure out how to get a VCF file out. A what what now? Exactly. When we try to obtain the sequence of some DNA the big machine that we dump our DNA does…

Why do we use ASCII files in genomics?

This rant was triggered when I was going over the format for FASTQ files. This is a pure rant: I propose no good solutions for anything here. I’m not even angry – just bemused. I’m a novice, so there are probably good reasons for keeping ASCII files for raw data which I just don’t know about. First,…

A lame adventure with progressiveCactus

Progressive Cactus is a set of tools that will align multiple DNA/protein sequences and save to the interesting HAL format. I decided to take it out for a spin. Compiling on Max OS Mavericks was easy (I just followed their Readme), except for this one problem with wget, but it was a easy fix. The command…