Comments on: Software Install – samtools-0.1.19 and stacks-1.37 http://onsnetwork.org/kubu4/2016/04/06/software-install-samtools-0-1-19-and-stacks-1-37/ University of Washington - Fishery Sciences - Roberts Lab Tue, 09 Apr 2019 18:37:58 +0000 hourly 1 http://wordpress.org/?v=4.0 By: Data Analysis – Oly GBS Data from BGI Using Stacks | Sam's Notebook http://onsnetwork.org/kubu4/2016/04/06/software-install-samtools-0-1-19-and-stacks-1-37/#comment-3943 Tue, 19 Apr 2016 15:19:03 +0000 http://onsnetwork.org/kubu4/?p=2070#comment-3943 […] Installed Stacks (and its dependencies on Hummingbird earlier today). […]

]]> By: kubu4 http://onsnetwork.org/kubu4/2016/04/06/software-install-samtools-0-1-19-and-stacks-1-37/#comment-3926 Fri, 08 Apr 2016 20:29:29 +0000 http://onsnetwork.org/kubu4/?p=2070#comment-3926

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!

]]> By: Katherine Silliman http://onsnetwork.org/kubu4/2016/04/06/software-install-samtools-0-1-19-and-stacks-1-37/#comment-3924 Fri, 08 Apr 2016 19:29:04 +0000 http://onsnetwork.org/kubu4/?p=2070#comment-3924 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.

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