Tag: perl

[Review] Unix and Perl to the Rescue

Unix and Perl to the Rescue is a light-hearted, compelling book that introduces key programming concepts and Unix tasks, particularly relevant to the field of Bioinformatics. It assumes no previous knowledge of Unix or Perl and presents step-by-step basic processes as well as the philosophy of well experienced […]

Converting FASTQ to FASTA

A little Perl one liner I borrowed from The Edwards Lab that converts FASTQ to FASTA. Please note I had to truncate the line to make it show properly in this blog entry.   $ cat file_to_covert.fq | perl -e \ ‘$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}’ \ > output.fasta Thanks Edwards Lab! I […]

A Script to Calculate GC content

Intermediate Perl GC content is a very interesting property of DNA sequences because it is correlated to repeats and gene deserts. A simple way to calculate GC content is to divide the sum of G and C letters by the total number of nucleotides in the sequence. Let’s […]

How to be a Biohacker

Biohackers embrace fully the philosophy of hackers: love for freedom, veneration of competence and utter curiosity for how things work. How does one become a biohacker? Usually biohackers cannot tell if they are really one of them until someone else says so. However, it is not enough to […]