Got a Fresh Apple?
How do I get my computer ready for Bioinformatics 2111? I just got a new Apple laptop, so I get to do a fresh start. By the time I get through 4 years with...
Author: admin
Microbial community analysis with QIIME2
This tutorial makes use of the data from the NC Urban Microbiome Project, a collaboration seeded by the Department of Bioinformatics and Genomics and involving participants from our department as well as Civil Engineering,...
Whole genome shotgun metagenomics with MetaPhLan
Like last week’s tutorial, this tutorial uses Urban Environmental Genomics Project data. The original version of the tutorial was developed by Anju Lulla for our student interns. Preparation and software installation You can use...
Gene expression analysis with DE-Seq
With many thanks to Anju Lulla — this is a modification of a protocol she used for the paper we are working on with our collaborators. To start off this lab, you should have...
Troubleshooting the read mapping lab
Hey everyone! A few people are reporting some trouble in making this lab work so I updated all my software and went in. I am just going to walk through what worked with one...
Expression quantitation with featurecounts
In this lab and the next, we are going to use two different methods to calculate differential expression for the same RNASeq dataset. Note: there is no standalone lab writeup due for the featurecounts...
Read mapping and variant calling
Mapping short sequence reads to a reference sequence is a common task in genomics. Many different results can be extracted from a mapped sequence, depending on the original experimental design that produced the sequence...
Pangenome analysis with PanX
PanX is a program for pangenome analysis and production of core genome phylogenies. The PanX analysis tools are available as a github package for custom genome analyses, and also as a web server. The...
Genome Comparison with Mauve
There are many ways to compare genomes, and these comparisons provide different kinds of information about evolutionary history and shared function. First, how do you decide which genes are “the same” across multiple genomes,...
Genome annotation with prokka
Why use Prokka? First, because in a benchmark test it has been shown to be as or more accurate at reproducing known annotation than RAST or xBASE2 in most annotation categories. Second, because it’s...