emBASE Tutorials
On this page you can find tutorials and information about emBASE functionalities and modules.
Presentations and Demos
- A 5 minutes screencast demonstrating how emBASE and Galaxy work together to easily analyse 24 sequencing libraries on EMBL cluster, in few clicks.
- emBASE Basic Operations (March 2015) : Sample annotations, Protocols, Assay/Experiment/Project management, interacting with the command line.
Tutorials / How-to
Submit your NGS Data to public repository (EBI Arrayexpress)
This page explains how to get your data ready for deposition in public repository.
Transfer Data to EBI ArrayExpress
Time to submit data to EBI? You first need to create the MAGE-TAB document. Here is then how you transfer files to EBI by FTP.
Import Analysis Results in emBASE
A new plug-in in emBASE is available. It allows you to store your result data for NGS experiments. An in-depth explanation can be found here.
With that plug-in, you can also upload a full analysis report folder as described here.
NGS Data Management
- A step-by-step tutorial on how to fill in the GCBridge form.
- Learn everything about Jemultiplexer, our awesome demultiplexing tool. Note that Jemultiplexer is also available in Galaxy.
- Managing your data files after the GCBridge (adding demultiplexed files, deleting lane files)
- Also see the JemBASE API page
- Locking and Unlocking your NGS files
- Positioning the Quality Control flag of your Sequencing assays (failed or success)
- Archiving files linked to experiment(s) or a project: copy sets of data files to e.g. tape, so that they can be removed them from the expensive storage space.
Biomaterial (samples, protocols ...)
- How to annotate samples for MIAME compliance : this how-to describes why and how you should annotate your experiment samples in emBASE to fit with MIAME rules. Sample annotation is required even if you batch uploaded your experiment using the BASELoader tool.
- How to annotate samples in batch using a tab-delimited file
How to annotate samples in batch using the new online spreadsheet editor
- Merge duplicate samples: A description about how to merge your samples, extracts, labeled extracts or sequencing libraries.
Experiments / Projects and Archiving Data to Tape
- Archiving files linked to experiment(s) or a project: copy sets of data files to e.g. tape, so that they can be removed them from the expensive storage space.
- How to annotate your experiment for MIAME compliance : describes why and how you should annotate your experiment in emBASE to match MIAME rules.
In Situ Images Module
- In situ storage: Storage and visualization of in situ assays
- Batch create ISH assays : this describes how you can prepare a spreadsheet to create multiple ISH assays in one click.
Microarray module
- How to access experiment data programmatically : this how-to describes how you can access raw data and meta-data (eg annotations) programmatically using the experiment view functionality
- Checklist before batch uploading data using BASELoader : this how-to describes how to prepare your data and what you should check before starting a batch upload.
- How to normalize your data : this how-to describes how you can normalize your raw data within emBASE. Note that MIAME compliant data submission to EBI's ArrayExpress requires to provide normalized data.
- Create new ResultFileFormat: this explains how to create a new result file format that is used to upload your raw data files into the emBASE database.
- The page CreateArrayDesign describes how to create a new array design for your experiment.
- Analyzing two channels arrays in emBASE. A powerpoint presentation by Julien Gagneur. In this presentation, Julien also shows how his plugins work. Note that screenshots have been made using old emBASE version and that the only difference compared to current version is the look & feel (i.e. layout colors) : Julien_BASE_17_03_06.ppt
- A BASE tutorial (for an older BASE version, few things have changed but still useful) created by Danny Park (from Harvard Medical School) : Overview of BASE capabilities by Danny Park PDF"
User Manuals
Guidelines
- Naming convention in emBASE : Get File
- MIAME Unit Symbol Table : Get File
- Guidelines on how to build a GAL file : Get File
Scripts/Helpers emBASE admins only
- Check if all RBA have a file in the rba-directory (array only)
- Port the folder structure for all old NGS assays
- Get a list of files and check if they exist in emBASE (ngs only)
- Get a list of all files and check if they exist in emBASE (array only)
- Get all files for raw data sets for a specific group
- How to create the fake emBASE installation
- Reload the sample count of sequence lanes
- Load the storage files for lanes, raw bio assays and images