Monthly Archives: August 2012

Workflow for Genome Resequencing and SNP Calling

Here is my current workflow for genome resequencing and SNP calling, culled from various helpfiles, internet sources, and of course, some things I have figured out myself:  

Posted in code

Extract Sequences from FASTA file.

So, I was trying to figure out a way of extracting significantly up regulated Transcripts from my Trinity assemblies. ¬†Low and behold, it’s possible with BioPython:

Posted in code

Count specific characters per line using AWK

I just figured out to use the handy little UNIX utility AWK, which makes parsing text files a breeze, if you know how to speak its language. For the uninitated, there is a great list of little AWK one liners

Posted in code