Genome Intelligence Blog

BINF 6203: GAGE tutorial

BINF 6203: GAGE tutorial

This lab is offered as an opportunity for extra credit or for your project requirement (if applicable). This was presented by Dr. Luo during a guest lecture visit last year, so there is not...

BINF 6203: Expression Statistics

BINF 6203: Expression Statistics

Last week you used transcriptome and read mapping tools to get read counts for your Vibrio vulnificus expression data, with two different pipelines. Now let’s analyze the data and get the top differentially expressed...

BINF 6203: Gene expression read quantitation

BINF 6203: Gene expression read quantitation

In this lab and the next, we are going to use two different methods to calculate differential expression for the same RNASeq dataset. In a nutshell, we have measured gene expression under two conditions...

BINF 6203: Annotation with RAST

BINF 6203: Annotation with RAST

In this lab exercise, you’ll use the myRAST software (or the RAST website) to annotate an assembled genome. Try this first with the E. coli genome assembly that you generated a couple of weeks...

BINF 6203: NGS Genome Assembly

BINF 6203: NGS Genome Assembly

Part 1: assemble a chloroplast genome Today’s first challenge is to assemble the chloroplast genome data that was generated by the BINF 6350 class. You do not have to assemble all of the chloroplasts...

BINF 6203: NGS Data QC

BINF 6203: NGS Data QC

Today, you’ll use trimming software to clean up several NGS data sets. We’ll take a look at the following: Chloroplast genome sequences generated by Spring 2014 BINF 6350 students. (Ion Torrent, single end) Some...

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...