If you have any questions about your submission, please get in touch with the Genomics help desk. Solving problems after sequencing takes a lot more work than avoiding those problems in the first place, so please take advice on anything you are unsure about.
From January 2024 we will be changing how we produce FASTQ files from sequencing runs. Please visit this page for the full implications of the change and links to Illumina's own documentation.
The spreadsheet for SLX submissions is available here.
Help for filling out this submission form is here.
The spreadsheet for submissions for sequencing on Oxford Nanopore sequencers (i.e. the PromethION) is available here.
Help for filling out this submission form is here.
The spreadsheet for submissions to the library preparation service is available here.
Help for filling out this submission form is here.
The spreadsheet for 10x single cell submissions is available here.
Help for filling out this submission form is here. There is also a more complete guide about the 10x options here.
We also have an FAQ for single cell experiments.
The spreadsheet for 10x Visium submissions is available here.
Help for filling out this submission form is here.
The spreadsheet for 10x Xenium submissions is available here.
Help for filling out this submission form is here.
The spreadsheet for direct submissions is available here.
Help for filling out this submission form is here. The page also contains instructions for how to start the sequencing run.
We have a guide to the use of custom primers. If you need to use custom primers for your sequencing, please read this guide first.
A full list of all the supported index types (kits) and indexes (barcodes) can be found on the index information page.
Fetching one's data after sequencing differs for researchers in CRUK-CI and those in external groups using the CRUK-CI sequencing service from other institutes. This page describes what you can expect to receive from the sequencing service and the two means of fetching your data onto your own machines.
BCL Convert handles UMIs differently to bcl2fastq, putting the UMI bases in the read header rather than a separate third read. This page will guide you through the changes and also contains links to Illumina's own documentation.
There is a guide for demultiplexing your data after its initial delivery available here. You may need to run demultiplexing again if you need more or less precise barcode identification, or if an error has been made with the indexing and some samples' data is in the lost reads files.
The sequencing service does not support demultiplexing your data a second time if an error is made with the indexes at submission. We cannot stress enough that the error to be avoided above all others in your submission is to give your samples the wrong indexes. Incorrect index information cannot be fixed in Clarity, and certainly not after sequencing (when the errors typically become apparent). The data stored in our archive (internal users only) will be forever wrong.