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July 31, 2019

Tutorial 02: How to upload your own data

In this video we will show you how to upload your own dataset. Note that fast genomics only accepts single cell gene expression data in sparse or dense matrix form. As a newly registered user, you do not yet have the permission to upload data. To get these rights, please contact us by email and we will assign the required user role to your account.

Let us now go to the datasets section. And click on this plus sign to begin the data upload process. A new window pops up, in which you specify the details of your data. The information you need to fill in are your contact details, as well as a title and description of the dataset. Further below, you can enter additional information such as a citation, and you find the dialog for the actual upload of your data files.

Let us quickly fill out the required information at the top before we move to the file upload. We begin the upload process with the expression matrix, which should be in a CSV or TSV plain text format. It may also be uploaded in a compressed version using zip or G-zip. We proceed to identify the organism that your data is sampled from. It is defined by the NCBI taxonomy ID, which you can look up after you follow the link.

Now the format of your data file needs to be defined. For the gene nomenclature you can choose from entrez ID, gene symbol and ensemble ID. Then you choose the format of your expression matrix. It can be either sparse or dense, and it needs a cell ID and the gene ID information in the first two dimensions. The next step is to select the current normalization of your data, for example counts, logarithmic counts, or others. If your data is not normalized, you should select counts.

It is advised to also upload cell and gene metadata files. These metadata can be arbitrarily complex and may contain information such as the donor, the source location of the sample, the batch or cohort information. Next, you can select the technology used to extract the data and – in case you have samples from different batches – you can select the corresponding cell metadata column in which this information is stored.

We have now entered all relevant information and are about to upload the data to fast genomics. Before you upload your data, please make sure that terms and conditions apply. OK, let’s start the upload.

Your data is now uploaded to fast genomics and we run some technical checks to make sure that the data fits into our database format. Depending on the size of your data, the dataset will soon appear in the list of datasets.

This concludes our tutorial on how to upload your own dataset. If you would like to know more, visit us at fast genomics dot org, where you can find the latest news and other tutorials to get you started. You can always get in touch with us via email or twitter, you can join our slack community, or visit us on YouTube or LinkedIn.

This video is provided through our YouTube channel.