Difference between revisions of "Pyrad"
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* The first stage is de-multiplexing your short read dataset using the barcodes, a processes which will generate new fastq file depending on the barcodes. This is done via: | * The first stage is de-multiplexing your short read dataset using the barcodes, a processes which will generate new fastq file depending on the barcodes. This is done via: | ||
pyrad -p params.txt -s 1 | pyrad -p params.txt -s 1 | ||
| − | * The second stage editing the raw reads for quality and is done via: | + | * The second stage editing the raw reads for quality, whereupon they will be converted to fast and is done via: |
pyrad -p params.txt -s 2 | pyrad -p params.txt -s 2 | ||
Revision as of 17:17, 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.
- If using a Gridengine job script, be sure to match the "-pe multi" value and number of CPUs in "params.txt" to have the same value.
- The first stage is de-multiplexing your short read dataset using the barcodes, a processes which will generate new fastq file depending on the barcodes. This is done via:
pyrad -p params.txt -s 1
- The second stage editing the raw reads for quality, whereupon they will be converted to fast and is done via:
pyrad -p params.txt -s 2
