Quick Start Guide

Quick Start Guide

mRNA-seq for Differential Expression in Eukaryotes Pipeline 2.4
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Platform Login
Log into your account any time by going towedge.maverixbio.com and entering your email address and the password you created when you activated your account.


wedge_login

Account Settings
To access your Account Settings, hover over “Account” at the upper right and click the “Settings” link. This will take you to the Account Settings page, where you can change your password, if needed, and Logout of your account. If you are associated with more than one account, you will see a list at the lower left where you can click on the account names to switch between them.

account_settings

Account Management
If you are an administrator of an account, you will see the “Manage User Roles” and “Invite a User” panels on the right. Managing user roles allows you to grant and revoke Admin permissions on your account, and remove users from your account to prevent them from having further access. When your account was initially created, members of the Maverix team had access to the account with Admin permissions in order to add datasets and provision genome browsers. You can now use the “Manage User Roles” panel to revoke their Admin access or remove them from your account entirely in order to increase security. If you need help from Team Maverix in the future, you can always invite one of us back onto the account temporarily to take care of any issues. It’s as simple as entering an email address from the “Invite a User” panel and clicking “Invite”.

invite_users

Dashboard
Once you’ve logged into your account, click Dashboard on the top navigation menu. This main landing page is where you can view the Projects, Shortcuts, and Activities panels, as well as the main navigation menu, which is located at the top of every page. We’ll cover each of these elements in more detail.

dashboard

Navigation Menu
There are four main sections within the Maverix Analytic Platform: Dashboard, Data, Explore and Results. You can navigate to these sections from the top of any page while you’re logged into your account. Hover over Project to reveal a list of your projects.

navigation

Projects
On the left side of Dashboard, the Projects panel is where you can create new projects and edit the text and content of your project descriptions.You can also navigate from project to project by clicking on the project description or image. This will change the content in the other Dashboard sections to reflect project-specific content. When you’re not at the Dashboard, you can change project content by hovering over Project on the Navigation Bar and selecting the project you need.

projects

Create and Edit Projects
To create a new project, click the New button in the Projects section, add a title and description, then save. You can add images and formatting using markdown language. To edit an existing project, select the project by clicking it in the Projects section, then click Edit and make any changes you need.

edit_project

Shortcuts & Activities
The Dashboard panels on the right contain Shortcuts and Activities. Shortcuts provide direct links to analysis results, including links to the genome browser, interactive tables and heat maps. Shortcuts can be customized and added by the account holder to make platform navigation easier. The Activities panel contains notifications, or alerts that require your attention.

shortcuts

Data
Click on Data from the navigation menu at the top of the page. This section will be where you can upload and view your input data files. The output files from your analysis will also be accessible from this section. Clicking on the column headers in your File Library allows you to sort your files by any column parameter.

mrnaseq_filelibrary

Uploading Files
It’s quick and secure to upload your files to the cloud from the Data tab. In the upper right, click the Upload Files button. From the upload page, click Add Files and select the files from your local computer. Once you have all the files selected and queued, click Start Upload. You can watch the progress as your files are uploaded to the cloud server, monitoring the data transferred and time remaining. The green Complete button will signal success!

uploadingfiles

Explore
The Explore section is where you can launch and monitor your analysis kits. If you’ve already launched an analysis, you can access the log outputs and monitor its progress by clicking on the analysis from the history. To launch a new analysis, click theStart New Analysis button at the upper right then pick the analysis kit you’d like to use.

analysis_history

Analysis Overview
Once you’ve selected an analysis kit, you’ll be taken to the analysis overview page. Shown here as an example is the mRNA-Seq for Differential Expression in Eukaryotes overview. The overview has a description of the analysis, list of references and the configuration panel. In addition, we include a list of open-source tools, benchmarking information, and a summary of the analysis protocol, with a description of the steps and resulting outputs.

AnalysisOverview

Monitoring Progress
Once you’ve launched the analysis, you can go back to the Explore tab and monitor its progress. Select your analysis from the execution history and view the analysis steps as they run or once they are completed. In this example, the analysis is complete, which can be seen by the green check marks next to each of the steps. You can open individual steps to read the status and view the output of the step. You can also look deeper by clicking Details and view the under the hood tool commands and parameters of the analysis.

 monitor

Results
As the analysis runs, some of the higher level outputs will be published to the Results section of the platform, including plots and bar charts that allow easy visualization and comparison between samples. In this example, the Expression Summary for four samples from an Exosome RNA-seq Analysis are viewed as pie charts on the Results tab.

 results

DATA SHEET

Whole Genome Sequencing Analysis
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Video

Whole Genome Sequencing Analysis

Description and walk through of Whole Genome Sequencing analysis on the Maverix Analytic Platform.

 

DATA SHEET

mRNA-seq for Differential Expression in Eukaryotes
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WHITE PAPER

RNA-Seq Open Source Tools 101
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APP NOTE

Pipeline Development for RNA-seq Analysis
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Video

mRNA-seq for Differential Expression in Eukaryotes

Description and walk through of mRNAseq for Differential Expression in Eukaryotes analysis on the Maverix Analytic Platform.

DATA SHEET

Small RNA-seq Analysis
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DATA SHEET

Exosome RNA-seq Analysis
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APP NOTE

Pipeline Development for RNA-seq Analysis
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Video

Exosome RNA-seq Analysis

A guided tour of the Maverix Biomics Exosome RNA-seq Analysis Kit, provided in partnership with the System Biosciences Exo-NGS service.

Product Documentation

DATA SHEET

mRNA-seq for Differential Expression in Eukaryotes
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DATA SHEET

Small RNA-seq Analysis
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DATA SHEET

Exosome RNA-seq Analysis
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WHITE PAPER

RNA-seq Open Source Tools 101
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APP NOTE

Pipeline Development for RNA-seq Analysis
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Help Documentation

Glossaries

External Resources