Getting Started

Information to get started on iMaps. Last updated 25th May 2022.

Running your own analysis

Making an account

To run your own analysis on iMaps you will need to make a free account. (Alternatively if you just want to browse publically available data you can "Explore as a guest").
To create an account, fill out the information on the home page:
You will immediately find yourself in the iMaps interface:
The iMaps interface.
Click on the "Upload Data" link in the left-most menu. You can upload any data here, but for a typical Demultiplex and Analyse run, you will need a Multiplexed FASTQ file and an Annotation spreadsheet (XLSX or CSV).
Spaces in file names are not permitted.
The upload portal.
Then, I will upload the annotation for my lane, currently you must save and upload this as csv or xls. You can download the annotation template here.
Some notes on the annotation - scientist is who did the experiment, both scientist and PI columns need to be the iMaps usernames of these people! These columns are optional in the case that you don't know. The protein/gene name needs to be the official name as found in Ensembl, or one of the other terms allowed in the second spreadsheet of the Excel template. The cell line must also be an official term - you can check the allowed terms in the second spreadsheet in the Excel template.
To request a new term, please post on our Slack workspace in #request-new-terms
You might have some errors that you need to correct - once the sheet has been validated it will be uploaded.
Now to run the main analysis pipeline you need to click on "Run Analysis" in the left-hand menu, followed by the "Demultiplex and Analyse" pipeline. Now you are prompted to add your annotation csv/xls and multiplexed fastq file.
For every species you are mapping to you will need to select the genome version - most of the time you will choose the Defaults.
After clicking "Run Command" you will be taken to a page where you can follow the progress of your analysis.