Step-by-Step Guide to Relatedness and Association Mapping Contents

Size: px
Start display at page:

Download "Step-by-Step Guide to Relatedness and Association Mapping Contents"

Transcription

1 Step-by-Step Guide to Relatedness and Association Mapping Contents OBJECTIVES... 2 INTRODUCTION... 2 RELATEDNESS MEASURES... 2 POPULATION STRUCTURE... 6 Q-K ASSOCIATION ANALYSIS K MATRIX COMPRESSION... 18

2 Objectives 1. Become familiar with relatedness measures in JMP Genomics 2. Learn about association mapping techniques that account for population structure and/or relatedness 3. Learn about compression of the K matrix Introduction Association mapping (also called association testing) is the statistical technique that tests each marker in the dataset for association with traits of interest. In agricultural data, association mapping is complicated by relatedness, or shared genetic backgrounds among the lines being studied. There are two kinds of relatedness that are described in this field: population structure and familial relatedness. The difference between these two is a matter of scale. Here we will describe how to assess relatedness among lines in a genetic marker dataset. Then, we will examine different techniques for performing association mapping in the context of population structure and/or familial relatedness. Lastly, we will explore a technique for simplifying and speeding up certain association mapping analysis by reducing the complexity of the model. Relatedness Measures In JMP Genomics there are two basic tools for computing and displaying relatedness among lines: Relationship Matrix and Kinship Matrix. The Relationship Matrix tool estimates the relationships among the lines using marker data, while the Kinship Matrix procedure takes pedigree information and computes the relationship measures directly. Output from either of these two procedures can serve as the K matrix, representing familial relatedness, in Q-K association analysis. Because pedigrees are generally not available in agricultural data, here we focus on the Relationship Matrix. 1. From the Genomics Starter menu, choose Genetics > Relatedness Measures > Relationship Matrix. 2. Find the dataset core_num_nodups.sas7bdat, and Choose it as the Input SAS Data Set. 3. Open the dataset and inspect it in JMP. It has 108 oat lines in rows, 28 columns of annotation and traits, and 601 columns with marker data. These markers are coded as numeric genotypes 0 is homozygous for the major allele, 2 is homozygous for the minor allele, and 1 is heterozygous. This numeric format is required for input to the Relationship Matrix procedure. Data in other formats should be converted to numeric genotypes using the Recode Genotypes procedure. 2

3 4. Select the Name variable from the Available Variables list, and place it into the ID Variables and Label Variable boxes. 5. Select all the non-marker variables, starting with Name and ending with Kolb_bydv, and place them in the box labeled Variables to Retain in Output Data Set. 6. In the box labeled List-Style Specification of SNP Variables, type num: (without the quotes) to select all variables starting with the prefix num. 7. Choose an Output Folder. 8. Examine the Analysis tab. Three different relationship metrics are available. Identity by Descent (IBD): Estimate of the probability that two lines share an allele that comes from the same ancestor Identity by State (IBS): Estimate of the probability that two lines share the same copy of an allele (not necessarily from the same ancestor) Allele Sharing Similarity: like IBS, with a slightly different calculation method (IBS uses range standardization, while Allele Sharing Similarity does not. 9. Leave the Identity by Descent option selected. 10. Check the Compute the Root of the Matrix by SVD box. This option produces a file containing the square root of the relationship matrix, which can be used later in the Q-K association analysis. 11. Uncheck the Perform Principal Components Analysis box. This Principal Components Analysis (PCA) option performs PCA on the computed relationship matrix, which can be useful for visualization and insight. This PCA should not be confused with the one used to compute a Q matrix for Q-K association, which is computed from the raw marker data. 3

4 12. The completed Analysis tab should look like the figure below: 13. On the Options tab, check the box labeled Plot Relationship Matrix Heat Map. 14. Click Run to start the analysis. 4

5 15. Examine the Heatmap Results in the first tab of the Results dashboard: The heatmap displays the relationships among the 108 lines. The red diagonal represents perfect relationship of each line with itself; the symmetric off-diagonal elements represent relationship measures (in this case IBD) for pairs of lines. The blocks of warmer colors on the diagonal show clusters of closely related lines. The dendrogram (tree diagram) on the right shows the results of a cluster analysis on the IBD matrix. Double click on any branch to zoom in and inspect the members. To revert to the top-level view, click on the Hierarchical Clustering hotspot and choose Release zoom. 16. Click the Heatmap Results drop-down menu in the Tabs panel, and choose View Data. If you scroll to the right in this table, you will see the IBD values in the columns with the IBD prefix. 17. Return to the Results dashboard, and view the IBD Pairs Results tab. The display shows the distribution of IBD scores for the 299 pairs of lines with IBD values greater than Inspect the list of pairs of lines with high IBD values by clicking the IBD Pairs Results drop-down menu, and choosing View Data. 19. Find the section on the left of the dashboard labeled Output SAS Data Sets, and click on the triangle to display the contents of this section. 5

6 20. A file named core_num_nodups_rm.sas7bdat is shown. This file contains the square root of the IBD matrix, to be used in Q-K association. This is different from the raw IBD values displayed in the heatmap. Population Structure Population structure is genetic similarity across large groups of individuals or lines and should be assessed in preparation for association mapping. Like familial relatedness, population structure can be incorporated into an association mapping analysis. In Q-K association analysis, population structure is modeled with a Q matrix, and familial relatedness is modeled with a K matrix. There are two ways to construct a Q matrix in JMP Genomics: Principal Components Analysis (PCA) and Multidimensional Scaling (MDS). We will discuss how to construct both types, starting with MDS. MDS is a technique for reducing a dataset with many variables (in this case, markers) into a smaller number of variables. Information is always lost when simplification occurs, but the MDS algorithm is designed to lose the least amount of information possible while reducing the complexity of a dataset. When performing MDS, the user must choose the appropriate number of dimensions for the reduced data, based on the results. 1. From the results dashboard of the previous Relationship Matrix analysis, click the Multidimensional Scaling button. The dialog for the MDS procedure is launched pre-populated with appropriate filenames and variable names from the previous analysis. 2. Choose Name from the available variables list, and place it into the Label Variable box using the arrow button. 3. Click on the Analysis tab. Change the Lower Number of Dimensions to Fit to 2, the Upper number of Dimensions to Fit to 10, and the Increment Between Upper and Lower Values to 2. These choices indicate that 5 different MDS solutions will be fit: 2, 4, 6, 8, and 10 dimensions. 4. Click Run to launch the analysis. 6

7 An overview of the MDS results is displayed: These plots show how the fidelity of the MDS fit improves as the number of dimensions allowed increases from 2 to 10. The user s job is to choose the solution that adequately represents the full data set in the smallest possible number of dimensions. This is a subjective decision, but the two plots here can help. Look for an elbow or a location in both plots where the rate of change decreases as the number of dimensions increase. In this example, 4 dimensions appears to be optimal. 5. Draw a box around the point representing 4 dimensions in either plot, and click the Display Clustered Heat Map button. The dashboard displays 2-D and 3-D plots of the 4 cluster solution, as well as a cluster analysis and heatmap. The data set behind these displays can be merged with the marker data for Q-K association analysis. Principal Components Analysis (PCA) is a data reduction technique similar to MDS, with some important differences. While MDS tries to reduce the data in such a way as to preserve the relationships among observations or lines, PCA is meant to describe the largest sources of variance in the data. As a result, PCA can be sensitive to smaller patterns, which would not be evident from MDS, found in a single maker or a handful of markers. 7

8 JMP Genomics can use PCA to control for population stratification in association testing in two ways. The first method, known as the Eigenstrat method, is found in the PCA for Population Stratification tool. This tool performs the PCA analysis first, saves the output, and then optionally performs Eigenstrat association analysis, if one or more trait variables are specified. The second method is to use PCA output as the Q matrix in a Q-K association analysis. This second method will be covered later in this document. 1. From the Genomics Starter menu, choose Genetics > GWAS Testing > PCA for Population Stratification. 2. Choose core_num_nodups.sas7bdat as the Input SAS Data Set. 3. Assign the four heading day variables (HD_ID, HD_MB, HD_ND, and HD_SK) as Trait Variables. 4. Assign Name as the Label Variable. 5. Type num: (without the quotation marks) in the box labeled List-Style Specification of Marker Variables. 6. Choose an Output Folder. 7. On the Annotation tab, use the Choose button to select core_num_nodups_anno.sas7bdat as the Annotation SAS Data Set. 8. Fill out the remainder of the Annotation tab as shown below: The Annotation Label Variable is the label that will be displayed in the graphical output for each marker. 8

9 The Marker Names Variable matches the names of the SNP columns in the marker data file, and is used to check that the order of the two files is consistent. The Annotation Group Variable and Annotation Location Variable are used to order and group the graphical output into separate chromosomes or linkage groups The Filter to Select Null SNPs is used when one knows of a group of markers that are not associated with the trait of interest. These unrelated markers can be named here to use only them in the PCA, increasing the precision of the Eigenstrat association analysis. 9. On the Options tab, check the box labeled Create Merged PCA Output Data Set. This option creates a file with both the PCA results and the original marker and trait data. This file can be used later for Q-K analysis. 10. Click Run to start the analysis. 11. When the results dashboard appears, click on the PCA 3D Row Scores tab to view this output. This output looks markedly different from the MDS output. The cloud of data points from the MDS analysis was roughly spherical, while the PCA output has a peculiar shape. This suggests that the PCA is picking out 9

10 small differences in the data and magnifying them. The MDS analysis might be a better choice for downstream Q-K association analysis. 12. Explore the Scree Plot. This plot is used similarly to the summary plots from the earlier MDS analysis. Look for the elbow in the plot to determine a sufficient number of dimensions for the analysis. 13. Click on the Summary Chart tab to view results from the Eigenstrat association analysis. The bar charts show statistical associations between the four traits and markers on multiple chromosomes. To interrogate a single chromosome at a time, find the button for that chromosome in the Tabs section and choose View Tab, or click the All P- Value Plots button. Or choose View Data from one of these buttons to look at the data table containing all the markers and significance results. Q-K Association Analysis Q-K association analysis was developed in order to perform association mapping while controlling for population structure and/or familial relatedness. The Q-K in this name refers to the two kinds of information that get included in the model. The Q matrix contains information about population structure, which can come from Multidimensional Scaling, Principal Components Analysis, or even manual assignment of the lines or individuals into groups curated by the user. The K matrix contains more fine-grained information about relatedness, usually IBD measures calculated from the marker data using the Relationship Matrix procedure. As in other kinds of association mapping, in Q-K association analysis an individual statistical model is created for each marker, using the trait as a dependent variable and the marker as an independent variable. The variables that constitute the Q and K matrices are also included in these models: Q variables as fixed effects, and K variables as random effects. Either the Q or the K variables may be omitted from the models, as desired. To run Q-K association analysis in JMP Genomics, one needs a datafile containing the traits to be analyzed, the marker genotypes, and the Q and K variables to be used in the analysis. An annotation dataset containing map information and any other marker information can also be used in the analysis this file is optional, but it is a good idea to include it. We will create the input data file for the Q-K analysis by joining the results files from the Relationship Matrix analysis and the Multidimensional Scaling analysis. 10

11 1. Use the File > Open command to open the Multidimensional Scaling results file with 4 dimensions, called core_num_nodups_ibd_mds4.sas7bdat. 2. Also Open the file with the square root of the IBD matrix from the Relationship Matrix procedure, called core_num_nodups_rm.sas7bdat. 3. With the file core_num_nodups_rm.sas7bdat in the foreground, select Tables > Join. 4. In the top left box, select the file core_num_nodups_ibd_mds4. 5. Check the box labeled Merge same name columns 6. Select the variable Name in the two Source Columns boxes, and then click the Match button. 7. Assign the Output table name as core_qk. The completed dialog should look like this: 8. Click OK to create the new joined file. 9. When the new data file appears, select File > Save As 10. Change the Save as type option to SAS Data Set, and click the Save button. 11. When the Alert popup window warns you about saving to other formats, click Yes. The file is complete, and ready for Q-K association analysis. 12. Choose Window > Close All to close all open data files and reports. 13. From the Genomics Starter menu, choose Genetics > Other Association Testing > Q-K Mixed Model. 11

12 14. Complete the General tab to match the figure below: 15. On the Q and K tab, type Dim: (without the quotation marks) in the List-Style Specification of Q Matrix Variables box, and type IBD: (without the quotation marks) in the List-Style Specification of K Matrix Square Root Variables box. 16. On the Model Variables tab, select Continuous for Type of Trait. 12

13 17. Fill out the Annotation tab to match the figure below. 18. On the Options tab, change the Format of SNP Variables to Numeric Genotypes. 19. Also on the Options tab, check the box labeled Output genotype LS means and diffs. 20. On the P-Value Plots tab, select FDR as the Multiple Testing Correction Using a multiple testing correction such as the False Discovery Rate (FDR) can help reduce the number of false positive results. Such corrections are routinely used in genome-wide association testing. 21. Click Run to start the analysis. 13

14 22. When the results dashboard opens, scroll through the charts on the Summary Chart page. The summary charts show the number of significant markers on each chromosome, separated by the four different traits. Note that there were no significant associations for HD_ID and HD_SK. The red bars represent results from the Genotype test, while the blue bars represent results from the Trend test. The trend test looks for a linear relationship in the trend scores when moving from homozygous minor to heterozygous to homozygous major, while the genotype test treats all genotypes as separate unordered categories. Note the Output SAS Data Sets section on the left side of the dashboard you can click on the gray triangle to expand the contents. This area has links to output files containing detailed statistical information about all the Q-K models. These files can be helpful in interpretation of results. 14

15 23. To see the significant markers that overlapped across the four traits for the genotype test, click the Genotype button in the Action Buttons section. There is a single marker that is significant in common between HD_MB and HD_ND. Let s investigate. 24. Click on the blue sector in the Venn diagram with the value 1. This sector is the intersection of the HD_MB and HD_ND traits. 25. Select Tables > Subset, and click OK in the new dialog. A new window opens with a data file consisting of a single row. This is the marker from the Venn diagram. The significant marker was on Chromosome 16A, with a position of roughly 56. Let s have a closer look at this chromosome. 15

16 26. Back on the Q-K Mixed Model results dashboard, click the button labeled Chromosome Ch_16A Results and select View Tab 27. Scroll down to the HD_ND trait, and draw a box around the point at the peak to select it. 28. Choose Tables > Subset to see information for the association test for this marker on the HD_ND trait. There two ways to run a Q-K analysis in JMP Genomics. The example we just worked through used the Q-K Mixed Model process, which is a general tool that has a great deal of flexibility, but requires you to construct the input dataset yourself. A simpler option is the Genetics Q-K Analysis Workflow, which performs all the steps for the Q- K analysis and merges the data automatically. It is, however, less flexible than the Q-K Mixed Model process: The workflow only allows a Q matrix computed from PCA, and a K matrix from IBD calculations from the Relationship Matrix process. Let s briefly work through a Q-K analysis using the workflow. The marker data file is core_num_nodups.sas7bdat, and the corresponding annotation file is core_num_nodups_anno.sas7bdat. 1. From the Genomics Starter menu, choose Genetics > Workflows > Genetics Q-K Analysis Workflow. 16

17 2. Complete the General tab as below: 3. Complete the Annotation tab as below: 4. Leave the default selections on the PCA Options and K Matrix Options tabs. 5. On the Model Variables tab, select the Continuous for Type of Trait. 17

18 6. On the Options tab, specify Numeric Genotypes for the Format of Marker Variables. 7. On the P-Value Plots tab, select FDR for Multiple Testing Correction. 8. Click Run to launch the analysis. When the workflow analysis is complete, a results journal will be displayed. Click on the Results links for each of the three processes to view the results. Note that the results of the Q-K association analysis are somewhat different from the previous version, which used MDS rather than PCA for the Q matrix variables. K Matrix Compression Q-K association analysis is computationally intensive, and it can take a very long time to analyze larger datasets. The part of the analysis that incorporates the K matrix is especially time consuming. The K matrix is square, so for every individual or line in the study, a corresponding K matrix variable must be added. In our example with 108 lines, there are 108 K matrix variables included in each model. There is a technique for reducing the number of variables required to represent the familial relatedness between lines. With fewer variables for each model, run time is significantly reduced. The technique is called K Matrix Compression (Zhang et al., 2010). It can be performed in JMP Genomics as part of the Genetics Q-K Analysis Workflow, or as a free-standing process. The algorithm optimizes the compression for one trait variable at a time, so it needs to be repeated for each trait to be analyzed. 18

19 Let s work through an example using the Genetics Q-K Analysis Workflow. We will add the K matrix compression to the previous analysis. 1. Find the journal from the previous Genetics Q-K Analysis Workflow. Click the button labeled Reopen GeneticsQKAnalysisWorkflow Dialog. The dialog for the workflow reopens, with the previous settings loaded. 2. On the General tab, remove all of the traits from the Trait Variables box except HD_MB. The K matrix can be compressed for only a single trait at a time. 3. Assign a new Output Folder to avoid overwriting the previous results. 4. On the K Matrix Options tab, check the box labeled Compress the K Matrix. 5. In the Compression Rate box, type 0.1 (without the quotes). This will cause the compression algorithm to evaluate solutions starting with all 108 variables, reducing the number by 10 percent each iteration. 6. Move the variable Name to the ID Variables box. 7. Click Run to start the analysis. 8. When the results journal appears, click on the Results link in the K Matrix Compression section. The plot shows the evaluation of different amounts of compression. The full, uncompressed K matrix is at the right side of the graph, with all 108 variables, and the amount of compression increases to the left. 19

20 The three criteria that are graphed have low values for better-fitting models. The lowest value for all three criteria occurs for the uncompressed K matrix at 108 clusters; however, the model with 20 clusters is nearly as good. Let s return to the dialog and force the algorithm to select 20 clusters. 9. Click the button labeled Reopen Dialog. The dialog for the K Matrix Compression process opens with the previous options loaded. Note that this is not the original workflow dialog; it is the standalone dialog for K Matrix Compression. The workflow shows a simplified interface for the standalone tool, now we are using the more complex and robust interface of the standalone tool. 10. Change the Compression Method to Automated. 11. Enter 20 (without the quotation marks) for the Number of Clusters for Automated Compression. 12. Click Run to start the analysis. 13. When the results appear, click the Q-K Mixed Model button. We are operating outside the workflow now, so we must launch each process individually. 14. Complete the Annotation tab as shown below: 20

21 15. On the P-Value Plots tab, select FDR as the Multiple Testing Correction. 16. Click Run to start the analysis. The results appear similar to the uncompressed analysis. 21

Step-by-Step Guide to Advanced Genetic Analysis

Step-by-Step Guide to Advanced Genetic Analysis Step-by-Step Guide to Advanced Genetic Analysis Page 1 Introduction In the previous document, 1 we covered the standard genetic analyses available in JMP Genomics. Here, we cover the more advanced options

More information

Genetic Analysis. Page 1

Genetic Analysis. Page 1 Genetic Analysis Page 1 Genetic Analysis Objectives: 1) Set up Case-Control Association analysis and the Basic Genetics Workflow 2) Use JMP tools to interact with and explore results 3) Learn advanced

More information

Step-by-Step Guide to Basic Genetic Analysis

Step-by-Step Guide to Basic Genetic Analysis Step-by-Step Guide to Basic Genetic Analysis Page 1 Introduction This document shows you how to clean up your genetic data, assess its statistical properties and perform simple analyses such as case-control

More information

Release Notes. JMP Genomics. Version 4.0

Release Notes. JMP Genomics. Version 4.0 JMP Genomics Version 4.0 Release Notes Creativity involves breaking out of established patterns in order to look at things in a different way. Edward de Bono JMP. A Business Unit of SAS SAS Campus Drive

More information

JMP Genomics. Release Notes. Version 6.0

JMP Genomics. Release Notes. Version 6.0 JMP Genomics Version 6.0 Release Notes Creativity involves breaking out of established patterns in order to look at things in a different way. Edward de Bono JMP, A Business Unit of SAS SAS Campus Drive

More information

Quality control of array genotyping data with argyle Andrew P Morgan

Quality control of array genotyping data with argyle Andrew P Morgan Quality control of array genotyping data with argyle Andrew P Morgan 2015-10-08 Introduction Proper quality control of array genotypes is an important prerequisite to further analysis. Genotype quality

More information

Expression Analysis with the Advanced RNA-Seq Plugin

Expression Analysis with the Advanced RNA-Seq Plugin Expression Analysis with the Advanced RNA-Seq Plugin May 24, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com

More information

Tutorial 7: Automated Peak Picking in Skyline

Tutorial 7: Automated Peak Picking in Skyline Tutorial 7: Automated Peak Picking in Skyline Skyline now supports the ability to create custom advanced peak picking and scoring models for both selected reaction monitoring (SRM) and data-independent

More information

Package lodgwas. R topics documented: November 30, Type Package

Package lodgwas. R topics documented: November 30, Type Package Type Package Package lodgwas November 30, 2015 Title Genome-Wide Association Analysis of a Biomarker Accounting for Limit of Detection Version 1.0-7 Date 2015-11-10 Author Ahmad Vaez, Ilja M. Nolte, Peter

More information

Estimating Variance Components in MMAP

Estimating Variance Components in MMAP Last update: 6/1/2014 Estimating Variance Components in MMAP MMAP implements routines to estimate variance components within the mixed model. These estimates can be used for likelihood ratio tests to compare

More information

Importing and Merging Data Tutorial

Importing and Merging Data Tutorial Importing and Merging Data Tutorial Release 1.0 Golden Helix, Inc. February 17, 2012 Contents 1. Overview 2 2. Import Pedigree Data 4 3. Import Phenotypic Data 6 4. Import Genetic Data 8 5. Import and

More information

COPYRIGHTED MATERIAL. Making Excel More Efficient

COPYRIGHTED MATERIAL. Making Excel More Efficient Making Excel More Efficient If you find yourself spending a major part of your day working with Excel, you can make those chores go faster and so make your overall work life more productive by making Excel

More information

Tutorial. OTU Clustering Step by Step. Sample to Insight. June 28, 2018

Tutorial. OTU Clustering Step by Step. Sample to Insight. June 28, 2018 OTU Clustering Step by Step June 28, 2018 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com ts-bioinformatics@qiagen.com

More information

Lab # 2 - ACS I Part I - DATA COMPRESSION in IMAGE PROCESSING using SVD

Lab # 2 - ACS I Part I - DATA COMPRESSION in IMAGE PROCESSING using SVD Lab # 2 - ACS I Part I - DATA COMPRESSION in IMAGE PROCESSING using SVD Goals. The goal of the first part of this lab is to demonstrate how the SVD can be used to remove redundancies in data; in this example

More information

Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation The American Journal of Human Genetics Supplemental Data Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation Chaolong Wang,

More information

Editing Parcel Fabrics Tutorial

Editing Parcel Fabrics Tutorial Editing Parcel Fabrics Tutorial Copyright 1995-2010 Esri All rights reserved. Table of Contents Tutorial: Getting started with parcel fabric editing...................... 3 Tutorial: Creating new parcels

More information

Bioinformatics - Homework 1 Q&A style

Bioinformatics - Homework 1 Q&A style Bioinformatics - Homework 1 Q&A style Instructions: in this assignment you will test your understanding of basic GWAS concepts and GenABEL functions. The materials needed for the homework (two datasets

More information

Week 7 Picturing Network. Vahe and Bethany

Week 7 Picturing Network. Vahe and Bethany Week 7 Picturing Network Vahe and Bethany Freeman (2005) - Graphic Techniques for Exploring Social Network Data The two main goals of analyzing social network data are identification of cohesive groups

More information

Intro to NGS Tutorial

Intro to NGS Tutorial Intro to NGS Tutorial Release 8.6.0 Golden Helix, Inc. October 31, 2016 Contents 1. Overview 2 2. Import Variants and Quality Fields 3 3. Quality Filters 10 Generate Alternate Read Ratio.........................................

More information

Recalling Genotypes with BEAGLECALL Tutorial

Recalling Genotypes with BEAGLECALL Tutorial Recalling Genotypes with BEAGLECALL Tutorial Release 8.1.4 Golden Helix, Inc. June 24, 2014 Contents 1. Format and Confirm Data Quality 2 A. Exclude Non-Autosomal Markers......................................

More information

Differential Expression Analysis at PATRIC

Differential Expression Analysis at PATRIC Differential Expression Analysis at PATRIC The following step- by- step workflow is intended to help users learn how to upload their differential gene expression data to their private workspace using Expression

More information

Statistical Analysis for Genetic Epidemiology (S.A.G.E.) Version 6.4 Graphical User Interface (GUI) Manual

Statistical Analysis for Genetic Epidemiology (S.A.G.E.) Version 6.4 Graphical User Interface (GUI) Manual Statistical Analysis for Genetic Epidemiology (S.A.G.E.) Version 6.4 Graphical User Interface (GUI) Manual Department of Epidemiology and Biostatistics Wolstein Research Building 2103 Cornell Rd Case Western

More information

The Lander-Green Algorithm in Practice. Biostatistics 666

The Lander-Green Algorithm in Practice. Biostatistics 666 The Lander-Green Algorithm in Practice Biostatistics 666 Last Lecture: Lander-Green Algorithm More general definition for I, the "IBD vector" Probability of genotypes given IBD vector Transition probabilities

More information

JMP Clinical. Getting Started with. JMP Clinical. Version 3.1

JMP Clinical. Getting Started with. JMP Clinical. Version 3.1 JMP Clinical Version 3.1 Getting Started with JMP Clinical Creativity involves breaking out of established patterns in order to look at things in a different way. Edward de Bono JMP, A Business Unit of

More information

Distances, Clustering! Rafael Irizarry!

Distances, Clustering! Rafael Irizarry! Distances, Clustering! Rafael Irizarry! Heatmaps! Distance! Clustering organizes things that are close into groups! What does it mean for two genes to be close?! What does it mean for two samples to

More information

Lecture 25: Review I

Lecture 25: Review I Lecture 25: Review I Reading: Up to chapter 5 in ISLR. STATS 202: Data mining and analysis Jonathan Taylor 1 / 18 Unsupervised learning In unsupervised learning, all the variables are on equal standing,

More information

Performing whole genome SNP analysis with mapping performed locally

Performing whole genome SNP analysis with mapping performed locally BioNumerics Tutorial: Performing whole genome SNP analysis with mapping performed locally 1 Introduction 1.1 An introduction to whole genome SNP analysis A Single Nucleotide Polymorphism (SNP) is a variation

More information

USER S MANUAL FOR THE AMaCAID PROGRAM

USER S MANUAL FOR THE AMaCAID PROGRAM USER S MANUAL FOR THE AMaCAID PROGRAM TABLE OF CONTENTS Introduction How to download and install R Folder Data The three AMaCAID models - Model 1 - Model 2 - Model 3 - Processing times Changing directory

More information

Package GWAF. March 12, 2015

Package GWAF. March 12, 2015 Type Package Package GWAF March 12, 2015 Title Genome-Wide Association/Interaction Analysis and Rare Variant Analysis with Family Data Version 2.2 Date 2015-03-12 Author Ming-Huei Chen

More information

Classification. Vladimir Curic. Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University

Classification. Vladimir Curic. Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University Classification Vladimir Curic Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University Outline An overview on classification Basics of classification How to choose appropriate

More information

BICF Nano Course: GWAS GWAS Workflow Development using PLINK. Julia Kozlitina April 28, 2017

BICF Nano Course: GWAS GWAS Workflow Development using PLINK. Julia Kozlitina April 28, 2017 BICF Nano Course: GWAS GWAS Workflow Development using PLINK Julia Kozlitina Julia.Kozlitina@UTSouthwestern.edu April 28, 2017 Getting started Open the Terminal (Search -> Applications -> Terminal), and

More information

REAP Software Documentation

REAP Software Documentation REAP Software Documentation Version 1.2 Timothy Thornton 1 Department of Biostatistics 1 The University of Washington 1 REAP A C program for estimating kinship coefficients and IBD sharing probabilities

More information

Getting to the Fun Part 3: How to Prepare Your Data for Analysis JMP Discovery Conference - Frankfurt Mandy Chambers - SAS

Getting to the Fun Part 3: How to Prepare Your Data for Analysis JMP Discovery Conference - Frankfurt Mandy Chambers - SAS Getting to the Fun Part 3: How to Prepare Your Data for Analysis JMP Discovery Conference - Frankfurt Mandy Chambers - SAS JMP 14 has the functionality to import multiple files into a single data table,

More information

Function. Description

Function. Description Function Check In Get / Checkout Description Checking in a file uploads the file from the user s hard drive into the vault and creates a new file version with any changes to the file that have been saved.

More information

QTX. Tutorial for. by Kim M.Chmielewicz Kenneth F. Manly. Software for genetic mapping of Mendelian markers and quantitative trait loci.

QTX. Tutorial for. by Kim M.Chmielewicz Kenneth F. Manly. Software for genetic mapping of Mendelian markers and quantitative trait loci. Tutorial for QTX by Kim M.Chmielewicz Kenneth F. Manly Software for genetic mapping of Mendelian markers and quantitative trait loci. Available in versions for Mac OS and Microsoft Windows. revised for

More information

Programming Exercise 7: K-means Clustering and Principal Component Analysis

Programming Exercise 7: K-means Clustering and Principal Component Analysis Programming Exercise 7: K-means Clustering and Principal Component Analysis Machine Learning May 13, 2012 Introduction In this exercise, you will implement the K-means clustering algorithm and apply it

More information

Tutorial. OTU Clustering Step by Step. Sample to Insight. March 2, 2017

Tutorial. OTU Clustering Step by Step. Sample to Insight. March 2, 2017 OTU Clustering Step by Step March 2, 2017 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com AdvancedGenomicsSupport@qiagen.com

More information

wgmlst typing in the Brucella demonstration database

wgmlst typing in the Brucella demonstration database BioNumerics Tutorial: wgmlst typing in the Brucella demonstration database 1 Introduction This guide is designed for users to explore the wgmlst functionality present in BioNumerics without having to create

More information

SAS Visual Analytics 8.2: Getting Started with Reports

SAS Visual Analytics 8.2: Getting Started with Reports SAS Visual Analytics 8.2: Getting Started with Reports Introduction Reporting The SAS Visual Analytics tools give you everything you need to produce and distribute clear and compelling reports. SAS Visual

More information

Tutorial. Identification of Variants Using GATK. Sample to Insight. November 21, 2017

Tutorial. Identification of Variants Using GATK. Sample to Insight. November 21, 2017 Identification of Variants Using GATK November 21, 2017 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com AdvancedGenomicsSupport@qiagen.com

More information

Network Traffic Measurements and Analysis

Network Traffic Measurements and Analysis DEIB - Politecnico di Milano Fall, 2017 Introduction Often, we have only a set of features x = x 1, x 2,, x n, but no associated response y. Therefore we are not interested in prediction nor classification,

More information

Introduction to GDS. Stephanie Gogarten. July 18, 2018

Introduction to GDS. Stephanie Gogarten. July 18, 2018 Introduction to GDS Stephanie Gogarten July 18, 2018 Genomic Data Structure CoreArray (C++ library) designed for large-scale data management of genome-wide variants data format (GDS) to store multiple

More information

Tutorial:OverRepresentation - OpenTutorials

Tutorial:OverRepresentation - OpenTutorials Tutorial:OverRepresentation From OpenTutorials Slideshow OverRepresentation (about 12 minutes) (http://opentutorials.rbvi.ucsf.edu/index.php?title=tutorial:overrepresentation& ce_slide=true&ce_style=cytoscape)

More information

Creating and Using Genome Assemblies Tutorial

Creating and Using Genome Assemblies Tutorial Creating and Using Genome Assemblies Tutorial Release 8.1 Golden Helix, Inc. March 18, 2014 Contents 1. Create a Genome Assembly for Danio rerio 2 2. Building Annotation Sources 5 A. Creating a Reference

More information

Getting Started with DADiSP

Getting Started with DADiSP Section 1: Welcome to DADiSP Getting Started with DADiSP This guide is designed to introduce you to the DADiSP environment. It gives you the opportunity to build and manipulate your own sample Worksheets

More information

Crop Counting and Metrics Tutorial

Crop Counting and Metrics Tutorial Crop Counting and Metrics Tutorial The ENVI Crop Science platform contains remote sensing analytic tools for precision agriculture and agronomy. In this tutorial you will go through a typical workflow

More information

Tutorial: Resequencing Analysis using Tracks

Tutorial: Resequencing Analysis using Tracks : Resequencing Analysis using Tracks September 20, 2013 CLC bio Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 Fax: +45 86 20 12 22 www.clcbio.com support@clcbio.com : Resequencing

More information

Clustering and Visualisation of Data

Clustering and Visualisation of Data Clustering and Visualisation of Data Hiroshi Shimodaira January-March 28 Cluster analysis aims to partition a data set into meaningful or useful groups, based on distances between data points. In some

More information

Tutorial. RNA-Seq Analysis of Breast Cancer Data. Sample to Insight. November 21, 2017

Tutorial. RNA-Seq Analysis of Breast Cancer Data. Sample to Insight. November 21, 2017 RNA-Seq Analysis of Breast Cancer Data November 21, 2017 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com AdvancedGenomicsSupport@qiagen.com

More information

A Content Based Image Retrieval System Based on Color Features

A Content Based Image Retrieval System Based on Color Features A Content Based Image Retrieval System Based on Features Irena Valova, University of Rousse Angel Kanchev, Department of Computer Systems and Technologies, Rousse, Bulgaria, Irena@ecs.ru.acad.bg Boris

More information

Gegenees genome format...7. Gegenees comparisons...8 Creating a fragmented all-all comparison...9 The alignment The analysis...

Gegenees genome format...7. Gegenees comparisons...8 Creating a fragmented all-all comparison...9 The alignment The analysis... User Manual: Gegenees V 1.1.0 What is Gegenees?...1 Version system:...2 What's new...2 Installation:...2 Perspectives...4 The workspace...4 The local database...6 Populate the local database...7 Gegenees

More information

ELAI user manual. Yongtao Guan Baylor College of Medicine. Version June Copyright 2. 3 A simple example 2

ELAI user manual. Yongtao Guan Baylor College of Medicine. Version June Copyright 2. 3 A simple example 2 ELAI user manual Yongtao Guan Baylor College of Medicine Version 1.0 25 June 2015 Contents 1 Copyright 2 2 What ELAI Can Do 2 3 A simple example 2 4 Input file formats 3 4.1 Genotype file format....................................

More information

QDA Miner. Addendum v2.0

QDA Miner. Addendum v2.0 QDA Miner Addendum v2.0 QDA Miner is an easy-to-use qualitative analysis software for coding, annotating, retrieving and reviewing coded data and documents such as open-ended responses, customer comments,

More information

Piping & Instrumentation Diagrams

Piping & Instrumentation Diagrams Page 1 Piping & Instrumentation Diagrams Preface Using This Guide What's New? Getting Started Entering the Workbench Setting up Working Units and Grid Placing Components Routing a Piping Line or I & C

More information

GenViewer Tutorial / Manual

GenViewer Tutorial / Manual GenViewer Tutorial / Manual Table of Contents Importing Data Files... 2 Configuration File... 2 Primary Data... 4 Primary Data Format:... 4 Connectivity Data... 5 Module Declaration File Format... 5 Module

More information

OTU Clustering Using Workflows

OTU Clustering Using Workflows OTU Clustering Using Workflows June 28, 2018 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com ts-bioinformatics@qiagen.com

More information

SOLOMON: Parentage Analysis 1. Corresponding author: Mark Christie

SOLOMON: Parentage Analysis 1. Corresponding author: Mark Christie SOLOMON: Parentage Analysis 1 Corresponding author: Mark Christie christim@science.oregonstate.edu SOLOMON: Parentage Analysis 2 Table of Contents: Installing SOLOMON on Windows/Linux Pg. 3 Installing

More information

1. Mesh Coloring a.) Assign unique color to each polygon based on the polygon id.

1. Mesh Coloring a.) Assign unique color to each polygon based on the polygon id. 1. Mesh Coloring a.) Assign unique color to each polygon based on the polygon id. Figure 1: The dragon model is shown rendered using a coloring scheme based on coloring each triangle face according to

More information

DNS Server Status Dashboard

DNS Server Status Dashboard The Cisco Prime IP Express server status dashboard in the web user interface (web UI) presents a graphical view of the system status, using graphs, charts, and tables, to help in tracking and diagnosis.

More information

ONLINE TUTORIAL T1: TEXT MINING PROJECT

ONLINE TUTORIAL T1: TEXT MINING PROJECT Online Tutorial T1: Text Mining Project T1-1 ONLINE TUTORIAL T1: TEXT MINING PROJECT The sample data file 4Cars.sta, available at this Web site contains car reviews written by automobile owners. Car reviews

More information

Importing data in a database with levels

Importing data in a database with levels BioNumerics Tutorial: Importing data in a database with levels 1 Aim In this tutorial you will learn how to import data in a BioNumerics database with levels and how to replicate and summarize level-specific

More information

Stats fest Multivariate analysis. Multivariate analyses. Aims. Multivariate analyses. Objects. Variables

Stats fest Multivariate analysis. Multivariate analyses. Aims. Multivariate analyses. Objects. Variables Stats fest 7 Multivariate analysis murray.logan@sci.monash.edu.au Multivariate analyses ims Data reduction Reduce large numbers of variables into a smaller number that adequately summarize the patterns

More information

ToCatchAThief c ryan campbell & jenn coughlan 7/23/2018

ToCatchAThief c ryan campbell & jenn coughlan 7/23/2018 ToCatchAThief c ryan campbell & jenn coughlan 7/23/2018 Welcome to the To Catch a Thief: With Data! walkthrough! https://bioconductor.org/packages/devel/ bioc/vignettes/snprelate/inst/doc/snprelatetutorial.html

More information

MQLS-XM Software Documentation

MQLS-XM Software Documentation MQLS-XM Software Documentation Version 1.0 Timothy Thornton 1 and Mary Sara McPeek 2,3 Department of Biostatistics 1 The University of Washington Departments of Statistics 2 and Human Genetics 3 The University

More information

Statistics 202: Data Mining. c Jonathan Taylor. Week 8 Based in part on slides from textbook, slides of Susan Holmes. December 2, / 1

Statistics 202: Data Mining. c Jonathan Taylor. Week 8 Based in part on slides from textbook, slides of Susan Holmes. December 2, / 1 Week 8 Based in part on slides from textbook, slides of Susan Holmes December 2, 2012 1 / 1 Part I Clustering 2 / 1 Clustering Clustering Goal: Finding groups of objects such that the objects in a group

More information

CHAPTER 6. The Normal Probability Distribution

CHAPTER 6. The Normal Probability Distribution The Normal Probability Distribution CHAPTER 6 The normal probability distribution is the most widely used distribution in statistics as many statistical procedures are built around it. The central limit

More information

Tutorial 01 Quick Start Tutorial

Tutorial 01 Quick Start Tutorial Tutorial 01 Quick Start Tutorial Homogeneous single material slope No water pressure (dry) Circular slip surface search (Grid Search) Intro to multi scenario modeling Introduction Model This quick start

More information

BGGN-213: FOUNDATIONS OF BIOINFORMATICS (Lecture 14)

BGGN-213: FOUNDATIONS OF BIOINFORMATICS (Lecture 14) BGGN-213: FOUNDATIONS OF BIOINFORMATICS (Lecture 14) Genome Informatics (Part 1) https://bioboot.github.io/bggn213_f17/lectures/#14 Dr. Barry Grant Nov 2017 Overview: The purpose of this lab session is

More information

Creating a custom mappings similarity matrix

Creating a custom mappings similarity matrix BioNumerics Tutorial: Creating a custom mappings similarity matrix 1 Aim In BioNumerics, character values can be mapped to categorical names according to predefined criteria (see tutorial Importing non-numerical

More information

For Research Use Only. Not for use in diagnostic procedures.

For Research Use Only. Not for use in diagnostic procedures. SMRT View Guide For Research Use Only. Not for use in diagnostic procedures. P/N 100-088-600-02 Copyright 2012, Pacific Biosciences of California, Inc. All rights reserved. Information in this document

More information

Axiom Analysis Suite Release Notes (For research use only. Not for use in diagnostic procedures.)

Axiom Analysis Suite Release Notes (For research use only. Not for use in diagnostic procedures.) Axiom Analysis Suite 4.0.1 Release Notes (For research use only. Not for use in diagnostic procedures.) Axiom Analysis Suite 4.0.1 includes the following changes/updates: 1. For library packages that support

More information

MSA220 - Statistical Learning for Big Data

MSA220 - Statistical Learning for Big Data MSA220 - Statistical Learning for Big Data Lecture 13 Rebecka Jörnsten Mathematical Sciences University of Gothenburg and Chalmers University of Technology Clustering Explorative analysis - finding groups

More information

Annotating a single sequence

Annotating a single sequence BioNumerics Tutorial: Annotating a single sequence 1 Aim The annotation application in BioNumerics has been designed for the annotation of coding regions on sequences. In this tutorial you will learn how

More information

Analyzing Genomic Data with NOJAH

Analyzing Genomic Data with NOJAH Analyzing Genomic Data with NOJAH TAB A) GENOME WIDE ANALYSIS Step 1: Select the example dataset or upload your own. Two example datasets are available. Genome-Wide TCGA-BRCA Expression datasets and CoMMpass

More information

Petrel TIPS&TRICKS from SCM

Petrel TIPS&TRICKS from SCM Petrel TIPS&TRICKS from SCM Knowledge Worth Sharing Well Path Design Part II This TIPS&TRICKS is the second of a three part series intended to aid the geoscientist working in Petrel and tasked with providing

More information

GeneMarker HID Quick Start

GeneMarker HID Quick Start GeneMarker HID Quick Start Guide Upload Data Run Wizard Size Call Quality Review Edit Panel Compare & Analyze Save & Print Reports SoftGenetics Relationship Testing Start Your Project Open Data Open Data

More information

Tutorial: De Novo Assembly of Paired Data

Tutorial: De Novo Assembly of Paired Data : De Novo Assembly of Paired Data September 20, 2013 CLC bio Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 Fax: +45 86 20 12 22 www.clcbio.com support@clcbio.com : De Novo Assembly

More information

WhatsUp Gold 2016 Application Performance Monitoring

WhatsUp Gold 2016 Application Performance Monitoring WhatsUp Gold 2016 Application Performance Monitoring Contents Introduction 1 Overview... 1 APM Terminology... 2 APM licensing and user rights... 3 Getting started with APM... 3 Application Profiles...

More information

User Manual for GIGI v1.06.1

User Manual for GIGI v1.06.1 1 User Manual for GIGI v1.06.1 Author: Charles Y K Cheung [cykc@uw.edu] Ellen M Wijsman [wijsman@uw.edu] Department of Biostatistics University of Washington Last Modified on 1/31/2015 2 Contents Introduction...

More information

GenomeStudio Software Release Notes

GenomeStudio Software Release Notes GenomeStudio Software 2009.2 Release Notes 1. GenomeStudio Software 2009.2 Framework... 1 2. Illumina Genome Viewer v1.5...2 3. Genotyping Module v1.5... 4 4. Gene Expression Module v1.5... 6 5. Methylation

More information

Hierarchical clustering

Hierarchical clustering Hierarchical clustering Rebecca C. Steorts, Duke University STA 325, Chapter 10 ISL 1 / 63 Agenda K-means versus Hierarchical clustering Agglomerative vs divisive clustering Dendogram (tree) Hierarchical

More information

Devyser QF-PCR. Guide to Sample Runs, Data Analysis & Results Interpretation

Devyser QF-PCR. Guide to Sample Runs, Data Analysis & Results Interpretation Devyser QF-PCR Guide to Sample Runs, Data Analysis & Results Interpretation Version 4-2013 Contents 1. Setting up a sample run on an ABI Genetic Analyzer... 3 1.1 Introduction... 3 1.2 Workflow... 3 1.3

More information

Dimension reduction : PCA and Clustering

Dimension reduction : PCA and Clustering Dimension reduction : PCA and Clustering By Hanne Jarmer Slides by Christopher Workman Center for Biological Sequence Analysis DTU The DNA Array Analysis Pipeline Array design Probe design Question Experimental

More information

SUM - This says to add together cells F28 through F35. Notice that it will show your result is

SUM - This says to add together cells F28 through F35. Notice that it will show your result is COUNTA - The COUNTA function will examine a set of cells and tell you how many cells are not empty. In this example, Excel analyzed 19 cells and found that only 18 were not empty. COUNTBLANK - The COUNTBLANK

More information

Digitising a map in arcgis desktop 10.3

Digitising a map in arcgis desktop 10.3 Digitising a map in arcgis desktop 10.3 1 CONTENTS 2 Evaluating your map... 2 3 Setting up the base map... 3 4 Georeferencing your map/maps... 3 4.1 Georeferencing tips.... 4 5 Digitising your maps...

More information

MicroStrategy Academic Program

MicroStrategy Academic Program MicroStrategy Academic Program Creating a center of excellence for enterprise analytics and mobility. DATA PREPARATION: HOW TO WRANGLE, ENRICH, AND PROFILE DATA APPROXIMATE TIME NEEDED: 1 HOUR TABLE OF

More information

Fusion Detection Using QIAseq RNAscan Panels

Fusion Detection Using QIAseq RNAscan Panels Fusion Detection Using QIAseq RNAscan Panels June 11, 2018 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com ts-bioinformatics@qiagen.com

More information

Chapter 6 Continued: Partitioning Methods

Chapter 6 Continued: Partitioning Methods Chapter 6 Continued: Partitioning Methods Partitioning methods fix the number of clusters k and seek the best possible partition for that k. The goal is to choose the partition which gives the optimal

More information

Guide to geometric morphometrics

Guide to geometric morphometrics Guide to geometric morphometrics Heidi Schutz, University of Colorado Jonathan Krieger, the Natural History Museum, London Version 0.4, 30 May, 2007. Copyright 2007 Relative warp analysis Programs The

More information

Solo 4.6 Release Notes

Solo 4.6 Release Notes June9, 2017 (Updated to include Solo 4.6.4 changes) Solo 4.6 Release Notes This release contains a number of new features, as well as enhancements to the user interface and overall performance. Together

More information

wgmlst typing in BioNumerics: routine workflow

wgmlst typing in BioNumerics: routine workflow BioNumerics Tutorial: wgmlst typing in BioNumerics: routine workflow 1 Introduction This tutorial explains how to prepare your database for wgmlst analysis and how to perform a full wgmlst analysis (de

More information

Ringtail Basics. Quick Start Guide

Ringtail Basics. Quick Start Guide Ringtail Basics Quick Start Guide Ringtail 8 brings a new level of simplicity, ease of use, and efficiency to document review. The following pages walk through scenarios, based on common tasks, to show

More information

Release Notes. Agilent CytoGenomics 2.7. Product Number. Key new features. Overview

Release Notes. Agilent CytoGenomics 2.7. Product Number. Key new features. Overview Release Notes Agilent CytoGenomics 2.7 Product Number G1662AA CytoGenomics Client 1 year named license (including Feature Extraction). This license supports installation of one client and server (to host

More information

Introduction to the New User Interface. ScienceLogic Beta Version 8.7.0

Introduction to the New User Interface. ScienceLogic Beta Version 8.7.0 Introduction to the New User Interface ScienceLogic Beta Version 8.7.0 Table of Contents Introduction to the New User Interface 4 Logging In and Out of the New User Interface 5 Using the Tabs in the New

More information

srap: Simplified RNA-Seq Analysis Pipeline

srap: Simplified RNA-Seq Analysis Pipeline srap: Simplified RNA-Seq Analysis Pipeline Charles Warden October 30, 2017 1 Introduction This package provides a pipeline for gene expression analysis. The normalization function is specific for RNA-Seq

More information

3. Cluster analysis Overview

3. Cluster analysis Overview Université Laval Multivariate analysis - February 2006 1 3.1. Overview 3. Cluster analysis Clustering requires the recognition of discontinuous subsets in an environment that is sometimes discrete (as

More information

CTL mapping in R. Danny Arends, Pjotr Prins, and Ritsert C. Jansen. University of Groningen Groningen Bioinformatics Centre & GCC Revision # 1

CTL mapping in R. Danny Arends, Pjotr Prins, and Ritsert C. Jansen. University of Groningen Groningen Bioinformatics Centre & GCC Revision # 1 CTL mapping in R Danny Arends, Pjotr Prins, and Ritsert C. Jansen University of Groningen Groningen Bioinformatics Centre & GCC Revision # 1 First written: Oct 2011 Last modified: Jan 2018 Abstract: Tutorial

More information

The software comes with 2 installers: (1) SureCall installer (2) GenAligners (contains BWA, BWA- MEM).

The software comes with 2 installers: (1) SureCall installer (2) GenAligners (contains BWA, BWA- MEM). Release Notes Agilent SureCall 4.0 Product Number G4980AA SureCall Client 6-month named license supports installation of one client and server (to host the SureCall database) on one machine. For additional

More information

Tutorial. De Novo Assembly of Paired Data. Sample to Insight. November 21, 2017

Tutorial. De Novo Assembly of Paired Data. Sample to Insight. November 21, 2017 De Novo Assembly of Paired Data November 21, 2017 Sample to Insight QIAGEN Aarhus Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.qiagenbioinformatics.com AdvancedGenomicsSupport@qiagen.com

More information

Pipe Networks CHAPTER INTRODUCTION OBJECTIVES

Pipe Networks CHAPTER INTRODUCTION OBJECTIVES CHAPTER 11 Pipe Networks INTRODUCTION Pipe networks are integral to a site-design solution. The piping system s complexity can vary from simple culverts to several storm and sanitary networks that service

More information