Hands-on - Registration of Managed Data¶
- 40 min
- Moderate
Overview
This hands-on accompanies users through the different steps necessary to load raw (managed) sequencing data. This includes:
- Accessing an initialised assay
- Registering the assay
We also show how to deal with:
- Large assays (>50 datasets)
- Assay that are multiplexed and not demultiplexed
Concepts
- Managed Data
- The concept of managed data is used to refer to data that as been generated by trusted data providers, for example GeneCore@EMBL
Walkthrough
In this walkthrough, we will be registering managed raw datasets. This situation arises when the data has been sequenced at Genecore@EMBL. A simplified pipeline is provided to register data coming from «trusted» providers, like internal core facilities.
Here, we review the different steps of this simplified pipeline, which is conceptually close to the other dataset registration pipelines seen in hands-on 101 and hands-on 102.
LabID retrieves data and initialises assays based on information sent by GeneCore
When the sequencing of your data is done, a message is sent to LabID by GeneCore - This is automated and occurs through APIs. GeneCore communicates the location of the files and the information accumulated about the assay. This compiles pieces of information given by the data owner upon ordering the sequencing, and pieces of information obtained from the sequencer (assay metadata). LabID receives all this information and initialises an assay for the user. The user then proceed with the registration, reporting the last missing bits.
Step 1. Create a new study¶
A new study needs to be created so the assay data can be assigned to it.
In the top menu:
- Click the new item button
- Click Dataset Management , then click Study
You now have been redirected to the New Study page.
Fill in the form:
- Set the name to Sequencing of XYZ
- Set you group project (Tea Project or Coffee Project)
Study creation form
Step 1. Navigate to the initialised assay¶
An Illumina Sequencing assay has been initialised for each trainee user. To find it:
In the left menu:
- Click Assays
- Click Illumina assays
You now have been redirected to the Assay List page.
On the Assay List page:
- Set the list page ownership filter to Personal
- Set the status column filter to
INITIALIZED
Assay list page filtered to find you own initialised assays
- Click the name
XYZ_PE_Man_4_1
You now have been redirected to the Assay Detail page.
Step 2. Start the registration wizard¶
Start the registration wizard from the Assay Detail page
In case an assay was wrongly initilised under your name
An assay can sometimes be assigned to the wrong owner. This is either expected (for example in the case where the lab technician orders the sequencing in place of the end user), or it is an error. In both cases, the assay ownership can be transferred.
Beware, sometimes an assay is shared. In these cases, assigning another user happens later in the wizard (on the Assign Sample page).
To transfer ownership, on the Assay Detail page of an assay with the INITIALIZED status:
- Click Not your data?
- Indicate the new user
- Click Confirm
On the Assay Detail page: - Click Register
You now have been redirected to the Registration Wizard for managed assay.
The managed assay registration wizard is a simplified version of the wizard seen in other registration hands-on. Most of the information has been communicated by the trusted provider and need to be reviewed (to spot potential mistakes). The remaining information bits need to be gathered from the user (mainly, study and sample name and barcode).
Step 3. Verify - Wizard (1/2)¶
At this step, in most cases (i.e. the assay contains few datasets, and the data already has been demultiplexed), there isn't anything to do except verifying the information transmitted by the data provider.
Verify a standard assay - few files, already demultiplexed
- Click Continue
There are two other situation possibly occurring:
- The data was not demultiplexed. Barcodes are needed for demultiplexing.
- The assay contains more than 50 datasets. Excel spreadsheet registration is advised.
Verify an assay that has not been demultiplexed - provide sample information
When multiplexed - not demultiplexed, the form displays a multiplexed checkbox checked, and a demultiplexed checkbox unchecked. In this cases, the number of sample needs to be indicated, and the sample name and barcodes need to be provided, following the format (coma delimited, 1 sample per line):
Verify a large assay containing more than 50 datasets
In the case the assay contains more than 50 datasets, it is advised to use excel spreadsheet registration. To do so:
-
- (1) Click Register with spreadsheet
- This opens up the excel registration form
- (2) Download the template spreadsheet by clicking Download template
- Fill it in locally
- (3) Upload the filled-in template back to the form - Click Browse... and select the local template file
- (4) Click Register assay to end the registration process
You now have been redirected to the wizard Assign Samples page.
Step 3. Assign Sample - Wizard (1/2)¶
The Assign Sample page is used to assign a sample to every dataset.
Create new samples or reuse existing ones
There are two different situations: Either the samples already exist (.e.g they have been previously created within an experiment, or created in the past for a different project but are used again to acquire new information), or they do not. In case they do not exist, they can automatically be created. By default, the dataset name is proposed as the sample name, but it can be adapted.
Also on the Assign Samples page:
- The owner of each dataset can be modified, in case the data is being loaded for different users.
- The Study can also be adjusted per dataset, in case more than one study was selected on the verify page
- Make sure to give meaningful sample names!
Here, we let the new samples be automatically created. Finish the registration by clicking Submit
You now have been redirected to the Assay Detail page of the registered assay