Genome Intelligence Blog

BINF 2111: Do SNPs make a difference

BINF 2111: Do SNPs make a difference

In the next script, we’ll combine the information from genomic FASTA file, GFF, and VCF to see if the variants change the protein sequence. The big challenge in this problem is integrating three sources...

BINF 2111: Protein translation

BINF 2111: Protein translation

Over the last few days, we’ve learned several pieces of python that will add up to a script that translates DNA into protein. Today’s lab is a little bit of a test — can...

BINF 2111: Genome Horoscope, Inc.

BINF 2111: Genome Horoscope, Inc.

Last week, you made a script that takes a “panel” of SNPs where a particular variant allele is associated with blue eyes in Europeans, parses an individual’s 23 and Me results to check their...

BINF 2111: Course plan

BINF 2111: Course plan

Welcome to Bioinformatics 2111/2111L. In this course, you’ll learn how to write simple executable UNIX scripts that automate “pipelines” of bioinformatics software, and to write scripts for genomic data analysis using the Python language....

BINF 2111: Opening and writing files in python

BINF 2111: Opening and writing files in python

Last week, we covered conditionals and comparators in python, and this morning we used them to test for sequence length, GC content, and presence of an “adapter”: DNASeq = raw_input(“Enter a DNA Sequence: “)...

BINF 2111: Exploring SNPs with bedtools (Lab)

BINF 2111: Exploring SNPs with bedtools (Lab)

We’re not quite ready to launch into full-on python scripting just yet — so here’s a little add-on to your final bash project, to help make use of the output files you generate. Why...

BINF 2111: Getting variable values from an input file (Lab)

BINF 2111: Getting variable values from an input file (Lab)

So far in your UNIX journey, you’ve learned how to: Run built-in and custom UNIX commands Put a series of commands together into a simple script that follows sequential logic, and construct a simple...

BINF 2111: Variant calling workflow (Homework)

BINF 2111: Variant calling workflow (Homework)

Now that you’ve implemented one workflow in a bash script, the challenge is to take the skills you’ve learned and implement a different script, on your own. The workflow that we’ll use is variant...

BINF 2111: looping, user input, and complex conditionals

BINF 2111: looping, user input, and complex conditionals

Today you are going to continue to work with your genome assembly script.  By the end of the lab period, you should have implemented the following features: Script loops through multiple *.fastq files, parsing...