Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology

Stutz WE, Bolnick DI

Date Published: December 9, 2014

DOI: http://dx.doi.org/10.5061/dryad.4fn4g.2

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title shell script to exectue commands for STC genotyping
Downloaded 29 times
Download runall.sh (885 bytes)
Details View File Details
Title R script for performing STC genotyping
Downloaded 49 times
Download stc.R (20.61 Kb)
Details View File Details
Title perl script for demultiplexing raw read data
Downloaded 34 times
Download readFNA.pl (9.578 Kb)
Details View File Details
Title Chimeras functions
Downloaded 21 times
Download chimeras_functions.R (7.923 Kb)
Details View File Details
Title R script to create 'barcodes' file for de-multiplexing
Downloaded 29 times
Description NOTE: This file is part of the original version of this data package. It is superfluous to the new version.
Download make_barcodes.R (339 bytes)
Details View File Details
Title R script to create "sequences" file for de-multiplexing
Downloaded 24 times
Download make_sequences.R (460 bytes)
Details View File Details
Title functions for stc.R
Downloaded 31 times
Download stc_functions.R (34.65 Kb)
Details View File Details
Title FASTA format file of raw sequence reads used to generate dataset described in the paper
Downloaded 22 times
Description This file contains the raw-read data from the 454 sequencing run used to produce the results in the paper. It can be used as input for readFNA.pl. Please see README.txt for more information.
Download reads.fna (70.65 Mb)
Details View File Details
Title empty fasta format file for de-multiplexing
Downloaded 23 times
Description Needed for de-multiplexing using readFNA.pl.
Download master.fasta (2 bytes)
Details View File Details
Title FASTA file of all unique amplicon sequences found in reads.fna
Downloaded 22 times
Description Contains all the unique amplicon sequences (no primers) along with numeric identifiers. This file is created from the output of readFNA.pl and make_sequences.R. It can be used as input for stc.R. Please see the README.txt file for more information.
Download sequences.fasta (8.042 Mb)
Details View File Details
Title table of samples and barcode IDs used in for genotyping
Downloaded 23 times
Description Contains rows designating the sample ID numbers and forward and reverse barcode ID numbers used for each sample genotyped in the paper. See barcode_sequences.csv for barcode nucleotide sequences. This file can be used as input for stc.R. Please see README.txt for more information and meta data.
Download sample_barcodes.csv (5.24 Kb)
Details View File Details
Title table of nucleotide sequences used as barcodes
Downloaded 17 times
Description Contains the sequences of all barcodes used to genotype samples described in the paper. Numeric ID numbers correspond to the ID numbers in samples_barcodes.csv. Can be used as input to the 'make_barcodes.R" script to create a list of barcode sequences for de-multiplexing. Please see README.txt for more information.
Download barcode_sequences.csv (939 bytes)
Details View File Details
Title table of processed reads from 454 sequencing run
Downloaded 31 times
Description Contains the output of running the readFNA.pl script on the included reads.fna input file. Output includes barcode IDs, seuqence IDs and indicates to which sample each read was assigned. Please see the README.txt file for meta-data and more information.
Download raw_reads.csv (50.62 Mb)
Details View File Details
Title post-genotyping data set used for analyses
Downloaded 26 times
Description Contains the output of stc.R after processing the samples described in the paper. Data includes the number of alleles for each sample and the presence/absence of each unique sequence within each sample. Please see the README.txt file for more information and meta-data
Download final_data.csv (228.6 Kb)
Details View File Details
Title README file for STC genotyping
Downloaded 42 times
Download README.txt (23.80 Kb)
Details View File Details

When using this data, please cite the original publication:

Stutz WE, Bolnick DI (2014) Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology. PLoS ONE 9(7): e100587. http://dx.doi.org/10.1371/journal.pone.0100587

Additionally, please cite the Dryad data package:

Stutz WE, Bolnick DI (2014) Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4fn4g.2
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Version History

Item Version Date Summary

* Selected Version

Search for data

Be part of Dryad

We encourage organizations to: