Tutorials for Genomics
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 MetaPhlAn can be...
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,...
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,...
This lab takes us back to the tomato chloroplast genome data again. You’ve QCed the chloroplast data, assembled it, mapped it, used it to learn genome track math with bedtools, and produced a consensus...
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...
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...
You can think of genomic data formats in a few main categories: Sequence data (FASTA, FASTQ) Alignments (BLAST results, SAM and BAM files) Track data (genomic intervals — coordinate range tracks, WIG files — continuous...
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...
In previous iterations of this course, we’ve used the RAST/SEED servers to perform annotation. RAST is a highly regarded genome annotation pipeline, and you will easily be able to justify using it to reviewers...
For today’s class, I have prepared a shared dropbox folder that contains the following items: sequence reads from one of the better chloroplast genome samples generated with our Ion Torrent instrument ERR008613 (a set...