Difference between revisions of "Poland Lab Wiki"

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== General Lab Information ==
 
== General Lab Information ==
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[[Lab Procedures]]
  
 
[[Reading List]]
 
[[Reading List]]
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[[Travel Instructions]]
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== Projects==
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[[NSF BREAD]]
  
 
== Genotyping Procedures ==
 
== Genotyping Procedures ==
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Lab protocols
 
Lab protocols
  
NGS Ordering
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[[Media:GBS_NGS_Service_Order_Quebec.pdf|NGS Ordering]]
  
GBS Data Management
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[[GBS Data Management]]
  
 
== High-Throughput Phenotyping Procedures ==
 
== High-Throughput Phenotyping Procedures ==
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[[UAS Phenotyping and Aerial Image Acquisition Procedures]]
 
[[UAS Phenotyping and Aerial Image Acquisition Procedures]]
  
UAS Field Data Collection Schedule
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[[UAS Phenotyping and Aerial Image Acquisition Procedure for DJI]]
  
[[UAS Data Management Procedures]]
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[[Media:UAV_Data_Upload_SOP_v1.3.pdf|UAS Data Management Procedures]]
  
UAS HTP Data Analysis
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[[UAS HTP Data Analysis]]
  
Land-based HTP Data Acquisition
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[[Media:CAMERAS_README.txt|Cameras README]]
  
Land-based HTP Data Collection Schedule
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== Research Methods ==
  
Land-based HTP Data Management
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[[Genomic Selection]]
  
Land-based HTP Data Analysis
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[[Meta-GWAS]]
  
== Lab Member Research Pages ==
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== Database ==
  
== Information Technology ==
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[[Connecting to the Database]]
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[[Media:Wheatgenetics_Quick_Start_Guide_ML_20171016.pdf|Wheatgenetics Database Quick Start Guide]]
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[[Media:DatabaseQueryFromR.pdf|Connecting to the Database with R]]
  
 
[[Genotyping Database]]
 
[[Genotyping Database]]
  
[[HTP Database]]
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[[Land-based High-Throughput Phenotyping Database]]
  
[[HTP Database Table Structure]]
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[[UAV High-Throughput Phenotyping Database]]
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[[Manual Phenotyping Database]]
  
 
[[Seed and Plant Database]]
 
[[Seed and Plant Database]]
  
== Equipment ==
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[[CIMMYT Wheat Breeding Database]]
  
For instructions on how to use the Toshiba Stake Printer and the Zebra Label printer see the links to the user manuals below. If you encounter any problems while using the printers, refer to the Troubleshooting sections in each manual.
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[[Media:CIMMYT_Automation_File_Interfaces.pdf|CIMMYT Database Import File Interface Specifications]]
  
[[Media:B-SX5T-R_Owners-Manual_EN.pdf|Toshiba Stake Printer User Manual]]
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== Scripts ==
  
[[Media:zt200series_userguide.pdf|Zebra Printer User Manual]]
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[[Tassel 5 GBS v2 Pipeline sample script for calling SNPs using reference genome]]
  
== Genomic Selection ==
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== Equipment ==
  
[[Media:GSquality_sbattenfield_033016.pdf|Genomic selection for quality PowerPoint]]
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The links below provide access to the user manuals for the Toshiba Stake Printer and the Zebra Label Printer.
  
[[Media:GS CV script.docx|Genomic selection example code]]
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If you encounter problems while using the printers please refer to the Troubleshooting section in the relevant user manual.
  
== Meta-GWAS ==
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[[Media:B-SX5T-R_Owners-Manual_EN.pdf|Toshiba Stake Printer User Manual]]
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 +
[[Media:zt200series_userguide.pdf|Zebra Printer User Manual]]
  
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== Guides ==
  
[[Media:MetaGWAS sbattenfield 033016.pdf|Meta-GWAS Methodology]]
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[[ How to Submit GBS Data to the NCBI Sequence Read Archive (SRA) ]]

Latest revision as of 20:04, 13 May 2020

Welcome to the Poland Lab Wiki!

General Lab Information

Lab Procedures

Reading List

Travel Instructions

Projects

NSF BREAD

Genotyping Procedures

Lab protocols

NGS Ordering

GBS Data Management

High-Throughput Phenotyping Procedures

UAS Phenotyping and Aerial Image Acquisition Procedures

UAS Phenotyping and Aerial Image Acquisition Procedure for DJI

UAS Data Management Procedures

UAS HTP Data Analysis

Cameras README

Research Methods

Genomic Selection

Meta-GWAS

Database

Connecting to the Database

Wheatgenetics Database Quick Start Guide

Connecting to the Database with R

Genotyping Database

Land-based High-Throughput Phenotyping Database

UAV High-Throughput Phenotyping Database

Manual Phenotyping Database

Seed and Plant Database

CIMMYT Wheat Breeding Database

CIMMYT Database Import File Interface Specifications

Scripts

Tassel 5 GBS v2 Pipeline sample script for calling SNPs using reference genome

Equipment

The links below provide access to the user manuals for the Toshiba Stake Printer and the Zebra Label Printer.

If you encounter problems while using the printers please refer to the Troubleshooting section in the relevant user manual.

Toshiba Stake Printer User Manual

Zebra Printer User Manual

Guides

How to Submit GBS Data to the NCBI Sequence Read Archive (SRA)