Uploading with Study Creation

Uploading during study creation

Step 1. Upload the study expression matrix

Load your study expression matrix file by filling an axis label to use when plotting expression and the following information:

1. Enter a description of the file here.
2. Species of the file being uploaded.
3. Indicate if the file is raw count (Yes) or normalized/processed measurements (No).
4. If raw count matrix is uploaded, specify the count type for the matrix (required).
5. Experimental input type of the biosample. Choose from "Whole cell", "Single Nuclei" or "Bulk"..
6. Library preparation protocol used for the loaded matrix file.
7. Modality of the expression data.
8. Select the format of the file being uploaded (it is selected for you automatically).

Note: "Skip"/"Next" will allow you to move forward and not add this file but your study will not have visualizations generated until this file is uploaded.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. This is a two step process, (1) the file is uploaded using the browser, then (2) the file is checked and loaded into the portal. Uploading a file can take a little time depending on the size of the file and your connection speed. During this step please do not navigate away from the page as it will cancel your upload. You are welcome to use your browser in other tabs or other windows of the browser. Checking and loading the file can take a while depending on the file size and type, so is done on our end and an email is sent to you on completion. Once the file has been loaded into the portal, it is then moved to the FireCloud workspace associated with your study.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Step 2. Upload the study metadata file

Upload your study metadata file; entering a description of the file/data contained in the file and selecting a file.

Note: "Skip"/"Next" will allow you to move forward and not add this file but your study will not have visualizations generated until this file is uploaded.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. The process for uploading and parsing files is the same as expression matrices. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Step 3. Upload cluster file

Load a cluster files by entering a name, a description of the ordination, entering axes for the plot, and choosing a file to upload. The name will be used to refer to the plot in the portal. The description should comment on the biology being displayed and the method generating the plot. The Z axis is optional and only used for 3D plots. You can also optionally provide the domain of each axis if you would like your plots to render a certain way. If not, the portal will size each plot automatically based on the input data provided.

You can load as many of these files as you would like.

Note: "Skip"/"Next" will allow you to move forward and not add this file but your study will not have visualizations generated until this file is uploaded.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. The process for uploading and parsing files is the same as expression matrices. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal. Feel free to use the "+ Add a Cluster File" button to add more files.

Step 4a. Fastq.gz data (Non-human)

Upload a couple, small fastqs If you are loading large or many files, there are better ways to upload to the portal (more here). Make sure "Primary Human Data" is set to No, enter a description, and click on "Choose File" to upload a compressed fastq. Please compress (gzip) your fastq files before loading. This is important to allow more efficient upload and download of data for portal users.

Note: "Next" will allow you to move forward and not add this type of file. You can add it later as needed.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. As before, the file will be uploaded into the portal and then sent to your FireCloud workspace. Please do not navigate away from the page while the upload is in process.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal. To add additional files select "+ Add a Fastq File", when complete select "Next".

Step 4b. Fastq.gz data (Human)

The portal should not store human sequence data, this should be stored in an external biological sequence archive of your choice and then linked to your portal study. After securely storing the data in an external repository, you may link that repository here. To store a link, select "Yes" for "Primary Human Data?". Add the link (URL) to the file or study, a name for the linked resource, a description of the sequenced sample(s), and click "Save". To add additional files select "+ Add a Fastq File", when complete select "Next".*

Note: "Next" will allow you to move forward and not add this type of file. You can add it later as needed.

Step 5. Gene lists

Load one or many gene lists by entering a name for the list, a description of the file, and choosing a gene list file to upload. Lists of genes are important results from transcriptome analysis. Many types of analysis produce a list or group of genes including genes that discriminate biological groupings or express in interesting or novel ways.

Note: "Next" will allow you to move forward and not add this type of file. You can add it later as needed.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. The process for uploading and parsing files is the same as expression matrices. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal. Feel free to use the "+ Add a Gene List File" button to add more files. When finished uploading files, click "Next".

Step 6. Miscellaneous

If you would like to share a file we have not mentioned so far, please share it here. Write a description of the file and choose a file to share.

Click "Upload & Save File", this will begin the upload of the file. A progress bar is given to help monitor the upload status. As before, the file will be uploaded into the portal and then sent to your FireCloud workspace. Please do not navigate away from the page while the upload is in process.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal. Feel free to use the "+ Add a Study File" button to add more files.

To complete the study upload process, click "Finish". You will always be able to come back to your study to add, update, and remove files.

Finished!

Done! You will now see a summary of your study. This will cover uploaded files, some information in your files like clusters, and study permissions, as well as links to your study in the portal and in FireCloud. If you loaded the required visualization files you may click on "View Study" and explore your data online!