Chapter 23 Bioinformatics for RAD seq data with and without a reference genome

We’ve gotta get our hands dirty with RAD and STACKS.

For some applications (like massive salamander genomes) this is the only way forward, at the moment. Can be useful, but is also fraught with peril.

Discuss all the problems, and strategies for dealing with them.

Note that stacks2 is a lot better than things were before. And, you can use a reference genome with them.

Amanda Stahlke gave a nice practical example at ConGen. Found all the materials on box through the link that Brian Hand gave me (in my email.)

That will be worth running through closely and carefully. Note that stacks2’s script now takes all the tsv output and puts it into a series of bams.