Posts tagged 'bioinformatics'

IGV: Null pointer exceptions, invalid GZIP header, invalid BZIP header

If you’ve run into a java.lang.NullPointerException or “Invalid Gzip Header” or some complaint about bzip while using the Integrative Genomics Viewer, then you’ve run into the same problem as me. Turns out I had too many index (*.bai) files that had similar naming to my *.bam files, and IGV assigned the wrong ones as the index, so whenever I tried to view reads from those samples, the index pointed to the wrong location in the bam, and one of those many errors would happen. So the solution is simple (and relatively fast): use samtools index on your bam files!

CodeNeuro NYC 2015

Last weekend I attended the CodeNeuro NYC conference, which is a conference for neuroscientists, programmers, and everything in between. It was a unique experience because it had both the excitement and energy of a tech conference, and the pure, unadulterated zest for knowledge of a scientific conference.

You can code, too!

Recently, I’ve had several conversations with biologists who know they should probably learn to code, but the whole concept is so daunting and they’re too busy with their research anyway. I’ve tried to convince them to pursue programming, not just because it’ll make their research analyses …

How to be fabulously successful: Eric Lander

Eric Lander, the visionary behind the Human Genome Project, a Professor of Biology at MIT and Systems Biology at Harvard, recipient of a MacArthur “genius” grant, and director of a world-renowned genome research institute, was recently interviewed for the New York Times newspaper. As a computational biologist and an avid …