Exporting data for the Bioinformatics Pipeline

For complete information on downloading data from FaceBase, please see our Exporting doc.

The following instructions are specific to using the Bioinformatics Pipeline.

Bulk Download of Sequencing Data

Bulk download of data from FaceBase is primarily supported by the “Export -> BAG” functionality on the FaceBase site. The instructions provided here are intended only for bulk download of sequencing data as required by the Hub and our partners that operate the Bioinformatics Pipeline.

With these instructions, you may download all of the raw sequencing data files (fastq) for RNA-seq and ChIP-seq experiments, on a per dataset basis.

1. You must have a FaceBase User account
   • Go to FaceBase and sign up
2. Install the client tools. See Deriva Clients.
   • Install DERIVA-Auth on your desktop computer
   • Install DERIVA Python (deriva-py) on the computer where you want to download the files to.
3. Establish an authentication token. See Authentication Tokens.
4. Download a copy of the fb-seq-bag.json download specification
   • If you want to do a dry run before really downloading an entire dataset, open the fb-seq-bag.json file and search-replace "download" with "fetch"
   • When you run the download client in the next step it will create a ‘fetch’ file that lists the files to be downloaded but will not actually download them
5. Pass the cookie during your cURL request to access files.

    $ deriva-download-cli www.facebase.org fb-seq-bag.json <output-dir> dataset=<dataset_RID>
   

   • where <output-dir> is the directory under which the downloaded files will be stored
   • and where <dataset_RID> is the dataset “RID” (e.g., ‘TMJ’)