Category: genomics

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,...

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

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: Read Mapping

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...

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...