Difference between revisions of "Pyrad"
| Line 12: | Line 12: | ||
The go-to tutorial for this is at: | The go-to tutorial for this is at: | ||
* http://nbviewer.jupyter.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD_3.0.ipynb | * http://nbviewer.jupyter.org/gist/dereneaton/1f661bfb205b644086cc/tutorial_RAD_3.0.ipynb | ||
| + | (note this tutorial assumes the executable is pyRAD, while in actuality, there are are only lower-case letter in the executable name). | ||
== highlights == | == highlights == | ||
| Line 19: | Line 20: | ||
* "pyrad -n" generates a "params.txt" file which contains settings for the run. A large part of the analysis can be configured by editing this file. | * "pyrad -n" generates a "params.txt" file which contains settings for the run. A large part of the analysis can be configured by editing this file. | ||
* The first stage is to gather statistics about your short read dataset and the barcodes. This is done via: | * The first stage is to gather statistics about your short read dataset and the barcodes. This is done via: | ||
| − | + | pyrad -p params.txt -s 1 | |
* The second stage editing the raw reads and is done via: | * The second stage editing the raw reads and is done via: | ||
| − | + | pyrad -p params.txt -s 2 | |
Revision as of 18:06, 20 April 2016
Introduction
Software for RADseq
module load pyrad
will load the necessary software, mainly muscle and vsearch.
Guides
The go-to tutorial for this is at:
(note this tutorial assumes the executable is pyRAD, while in actuality, there are are only lower-case letter in the executable name).
highlights
- with the pyrad module loaded, the "pyrad "executable is immediately available on the command line
- one of "-p", "-d", "-D" and "-n" options are essential.
- "pyrad -n" generates a "params.txt" file which contains settings for the run. A large part of the analysis can be configured by editing this file.
- The first stage is to gather statistics about your short read dataset and the barcodes. This is done via:
pyrad -p params.txt -s 1
- The second stage editing the raw reads and is done via:
pyrad -p params.txt -s 2
