Difference between revisions of "Stacks"
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* Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags". | * Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags". | ||
* Browse to [http://stacks.hpc.ufl.edu stacks.hpc.ufl.edu] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows: | * Browse to [http://stacks.hpc.ufl.edu stacks.hpc.ufl.edu] and use your HPC credentials to log in and view the results. The exact URI is constructed as follows: | ||
| − | http://stacks.hpc.ufl.edu/stacks/index.php?db=DATABASE | + | <nowiki>http://stacks.hpc.ufl.edu/stacks/index.php?db=DATABASE</nowiki> |
Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to [http://stacks.hpc.ufl.edu/index.php?db=tut_radtags http://stacks.hpc.ufl.edu/index.php?db=tut_radtags] for the output of a [http://creskolab.uoregon.edu/stacks/tut.php#pipe Stacks Tutorial]. | Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to [http://stacks.hpc.ufl.edu/index.php?db=tut_radtags http://stacks.hpc.ufl.edu/index.php?db=tut_radtags] for the output of a [http://creskolab.uoregon.edu/stacks/tut.php#pipe Stacks Tutorial]. | ||
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Revision as of 19:29, 21 August 2012
Description
Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.
Required Modules
Serial
- stacks
System Variables
- HPC_{{#uppercase:stacks}}_DIR - installation directory
Additional Information
The command line pipeline is available via the "stacks" module.
The web interface that can be used for visualizing genetic maps and correcting the analysis is being installed and tested as of Aug 21st, 2012.
To run stacks with database export:
- Log into a test node and load the stacks module:
- Create a database with a name that ends with "_radtags" using the 'hpc_create_stacks_db' script
hpc_create_stacks_db test1_radtags
The script will produce an error and quit if the database already exists.
- Log out of the test node.
- Run 'denovo_map.pl' as usual via a batch job specifying the database name with "-B test1_radtags".
- Browse to stacks.hpc.ufl.edu and use your HPC credentials to log in and view the results. The exact URI is constructed as follows:
http://stacks.hpc.ufl.edu/stacks/index.php?db=DATABASE
Substitute your own database name for 'DATABASE' at the end of the URI. To see an example view - go to http://stacks.hpc.ufl.edu/index.php?db=tut_radtags for the output of a Stacks Tutorial.