Getting ready to analyze our Ostrea lurida genotype-by-sequencing data and wanted to use the Stacks software.
We have an existing version of Stacks on Hummingbird (the Apple server blade I will be running this analysis on), but I figured I might as well install the latest version (stacks-1.37).
Additionally, Stacks requires samtools-0.1.19 to run, which we did NOT have installed.
I tracked all of this in the Jupyter (iPython) notebook below.
Due to permissions issues during installation, I frequently had to leave the Jupyter notebook to run “sudo” in bash. As such, the notebook is messy, but does outline the necessary steps to get these two programs installed.
Jupyter notebook: 20160406_STACKS_install.ipynb
NBviewer: 20160406_STACKS_install.ipynb
Will you be waiting for the genome to use Stacks, or doing de novo assembly? If de novo, I recommend you read the details on what the parameters for ustacks mean, especially the -M parameter:
http://catchenlab.life.illinois.edu/stacks/param_tut.php
You should definitely increase -M for ustacks and -n for cstacks. If you don’t want to wait for a genome, then I recommend setting -M to at least 8, then when you have a genome you can map the loci assembled by stacks to the genome in order to idenify potential paralogs that were grouped together.
Thanks for the info. Doing de novo for now. Already have ustacks running with defaults.
How did you figure out the settings you suggest?
As always, thanks for checking in on this stuff!