Running cellranger_scCloud
You will first need to create a study so there is a place to work with your file. When you create the study, make sure to you use a billing project that is not the Default Project. Note: if you would like to use our analysis test billing project that is free of charge, please contact us at scp-support@broadinstitute.zendesk.com.
Please see instructions here to create a study.
If you see the "Analysis" tab, you have a study that is set up correctly for you to run pipelines.
You will need to upload your csv file and the fastq.gz files from your sequencing run to your bucket associated with the study.
Here are instructions to upload to your bucket using gsutil.
Please note, it may be easier for you long term to collect all your fastqs.gz files in a "folder" in the bucket. This is simply done by adding the directory you want to copy to in the gsutil cp command (the directory will automatically be made for you).
# Initial example command
# If you were wanting to copy all fastq.gz files in your current directory and put them in the bucket
gsutil cp *.fastq.gz gs://xx-xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
# Modified example command
# Same as above but collecting the fastq.gz files in a "fastqs" directory in the bucket.
gsutil cp *.fastq.gz gs://xx-xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx/fastqs/
- Version info:
- CellRanger: 2.2.0
- scCloud: 0.6.0
You can come back to the submission history to check on the status your workflows. Feel free to refresh as needed.
Buttons:
View Run Info: View submission information.
Sync: Copy the run outputs over to the portal. These will gain the sharing permissions of your study (eg. if the study is private or public, the synced files will be private or public respectively).
Show Errors: Show errors associated with errored workflow runs.
Delete Submission: Delete the submission and outputs generated by the submission but not the inputs.
The portal is made to allow you to inspect your outputs of your pipelines before officially putting them in your study. This is particularly important if your study is public or shared, it gives you the ability to catch bad runs before publicizing or sharing the files.
After running a pipeline, you have access to the files if you want to inspect them, but you will need them to be "Sync"ed to the portal study before you can make interactive plots with them. Click the Sync button to select what files to link to the portal. A couple of quick details:
- You do not have to Sync all files.
- Un-Synced files will stay in your bucket unless deleted.
- You can sync some files now and some files later.
For every file found in the workspace, you will be prompted to provide details for each one. Depending on what type of file it is, the forms will update to match your selection. For 10X files we will make guesses for you on how you want to sync the run to optimize portal functionality. Feel free to edit or just use defaults. Click sync to sync each file. For more details, please read our sync detail page.
NOTE: If you do not want a file to show up in your study, you can either leave the form blank, or click "Don't Sync" to remove the form from the page. The portal will ignore that file for now. You can add it in at a later date if you wish by re-running the 'Sync Workspace' function for this study.
Here is an example form for syncing an expression matrix as well as the sync button to complete the action.
Ok, done! If you selected defaults, you should have a study full of interactive plots, metadata labels, and files to download and share.