Revision as of 17:22, 20 April 2016

Introduction

Software for RADseq

module load pyrad

will load the necessary software, mainly muscle and vsearch.

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).

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 fasta. This is done via:

pyrad -p params.txt -s 2

The third stage is about de-replicaiting (unsure as to meaning) and clustering the short reads. This is done via:

pyrad -p params.txt -s 3

@@ Line 24: / Line 24: @@
 * The second stage editing the raw reads for quality, whereupon they will be converted to fasta. This is done via:
   pyrad -p params.txt -s 2
+* The third stage is about de-replicaiting (unsure as to meaning) and clustering the short reads. This is done via:
+ pyrad -p params.txt -s 3