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GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

Radtag demultiplex samples

Community rating: ?????

This is a tool to demultiplex samples. It is part of the stacks suite of tools. It examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cut site are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some sequencing errors while eliminating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be specified on the command line (the threshold and window size can be adjusted).

Quick Start

To use demultiplex samples, import your data in fastq format.
Resources: http://creskolab.uoregon.edu/stacks/comp/process_radtags.php

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> demultiplex samples.

Input File(s)

Use barcodes_GBS_revised.txt and IBM/ directory from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input folder to get the output provided in the next section below.

Use Default parameters for all options, but in the Barcode Option Select "Barcode in line with sequence on single-end read"

Output File(s)

Expect a folder named samples that will contain 155 files named "samples_barcode.fq" where barcode is each of the barcodes used for multiplexing your samples. In the current example we have used 155 different barcodes that is why 155 different files are expected.

Tool Source for App

http://creskolab.uoregon.edu/stacks/comp/process_radtags.php

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radtag demultiplex samples (archived)