Uploading many FASTQ files

Uploading many FASTQ files at once

Overview

Depending on the assay, you may need to upload many FASTQ files to Single Cell Portal.  In this case, you most likely will not want to load each file individually. As a solution, we support loading tarred directories of files. Please make sure the extension on the tarred directory is .tar.fastq.gz .

We recommend dividing up FASTQ files into multiple directories based on batches (potentially based on biological cohorts) so that others need not download all of your files just to get a specific group of interest.

How to tar a directory in Linux

# Move to the directory using cd
cd /to/where/your/directory/is/located

# tar directory
# This will leave the original directory intact
# Note the additional directory will need extra space on your drive if this is large.
tar -czvf new_name.tar.fastq.gz directory_to_tar

How to tar a directory in Mac

Open up the application called "Terminal" at Applications/Utilities/Terminal and follow the instructions for Linux.

How to tar a directory in Windows

For Windows machines, you will need to download a program to create tar archives. Here is a great post to walk you through the process of making a GZip tar archive.

https://linhost.info/2012/08/gzip-files-in-windows