Getting things started

Starting a new single-cell analysis can feel like a daunting task at first, but here with Nygen Analytics, we will show you how easy it is to get your first dataset files uploaded!

To kickstart your single-cell journey, we will begin with the upload of single-cell count data. This can be in a matrix or table that contains the counts of features, e.g. genes, associated with each barcode or cell in a sample. Nygen Analytics platform supports a variety of file formats from different technologies such as 10x Genomics Cellranger, BD Rhapsody and kallisto bustools, so you can upload files from your own research or public datasets from your favourite publications, and allow you to focus on your analysis without the hassle of file format conversion.

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Steps:

1. To start uploading your first files, click on the Upload button from your empty project.

2. From the uploads page, you can drag and drop files from your file browser or click on the ‘Browse files to upload’ button.

3. Once the files appear loaded on the page, click on the ‘Start Upload’ button.

4. You will need to confirm that any files you are uploading are GDPR compliant and free from sensitive information, e.g. real patient names, ages etc. should not be uploaded.

5. You can upload more files or redirected to your Inbox page where you will find your uploads importing.

6. You can also check the progress for importing from the ‘Ongoing tasks’ cloud icon.

7. Once the dataset has been fully imported, you can use the checkbox to select the dataset and move it into a project.

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💡 Tips: Uploading MTX files

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Uploading files with multiple modalities

You can also upload CITE-seq data onto the platform. CITE-seq (cellular indexing of transcriptomes and epitopes) is a method of sequencing that captures both the transcriptomic data and cell surface proteins of single cells. During file uploads, we look for features that have the feature type ‘Antibody Capture’ and prompt the user for input whether we should treat them as ADT (antibody-derived tags) or HTO (hashtag oligos) data.

Steps

1. Select the files for upload from the upload page

2. Once the files are added, you will be asked to mark whether the ‘Antibody capture’ features detected in your file are antibody-derived tags (ADT) or hashtag oligos (HTO).

3. You can also upload files with both ADT and HTO data, and then choose the options accordingly when prompted.

4. Once the input has been saved you can continue as normal and start the upload.

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💡What happens when uploads fail?

If the file format was incompatible for upload onto the platform, our support team will be notified and the file can be checked manually.

• We will notify you by email once we receive the file uploads for manual checks. If you would like to cancel the upload and manual check, please contact support as soon as you can.
• Once the manual check is done, we will upload the file to your account or notify you by email if the file cannot be uploaded.

If the file was supported format and failed at importing, please get in touch with our support team and we will look into the issue.

Learn about which file formats are supported: Supported file formats

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