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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: 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...