Genome Intelligence Blog

Sequence Assembly

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...

Sequence Read QC

DNA Sequencing is a continually evolving technology, with new platforms becoming available each year, all designed with the aim of reducing the cost and increasing the speed of large sequencing projects. As you can...

BINF 6203: 16S rRNA classification with QIIME

This tutorial makes use of the data from the Urban Environmental Genomics Project, a collaboration seeded by the Department of Bioinformatics and Genomics and involving participants from our department as well as Civil Engineering,...

BINF 6203: Expression quantitation with featurecounts

BINF 6203: 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...

BINF 6203: Simple variant calling

BINF 6203: Simple variant calling

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...

BINF 6203: Genome track math

BINF 6203: Genome track math

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...

BINF 6203: Genome Comparison with Mauve

BINF 6203: 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,...