Stanford Functional
Genomics Facility

Receiving Your Data

Your results from sequencing runs performed at the Stanford Functional Genomics Facility are available either by direct download or transfer to portable, external hard drive(s).  Downloads are available by Secure FTP for investigators with access to the Stanford University network.  For those without Stanford network access or those who prefer the convenience (and delivery speed) of a portable hard drive, drives with your data will be provided for the cost of the drive and a nominal transfer charge. Shipment of drives can also be arranged.

If you choose to download your results, you will be provided with a download account and access information.  Please note that downloading large amounts of data (such as image sets) may be impractical unless you are on the local University network.   If you choose to receive to your data on hard disk, your data will be delivered on an eSATA/Firewire/USB 2.0 drive.  Current prices for hard drives (subject to change, most likely downward) are:

1 TB for $150
2 TB for $250
4 TB for $425

Data will be delivered on the lowest number of disks required to fit the data.  You may opt for a larger drive than is required for your data.  While we do not accept user provided drives for data transfer (to avoid interface, speed, and formatting issues), you may reuse SFGF supplied disks for future transfers. 

Examples:

  1. For a data set of 3.8 TB, results would be split across two separate 2 TB drives.

  2. For a data set of 400GB, you may select any of the above drive options. You may also return the disk to have future runs transferred to the available space on the disk if the free space is adequate.

  3. If your full data set (including images and cluster analysis) is 3.8 TB but you wish only to retain the base calls and one reference genome alignment (no images or cluster analysis),   your base call data and a single alignment will likely fit on any of the above disk options. 

Data from runs will be available for download within one business day of run completion.  Disk drives will be ready for pickup within two business days.

How much data will I receive?

Each sequencing run generates the following data (in order of creation):

The amount of generated depends on the lane and cycle count for your analysis.  Some rules of thumb to estimate the amount of data generated are:

Images 3 GB per cycle per lane
Cluster Analysis 250 MB per cycle per lane
Base Calls 25 MB per cycle per lane
Alignment 10 GB per lane

Example:

For a 76 cycle, 8 lane run,  a typical amount of data would be:

Images   76 x 8 x 3GB ~1.8 TB (1824 GB)
Cluster Analysis   76 x 8 x 250MB ~152 GB
Base Calls  76 x 8 x 25MB ~15 GB
Alignment   8 x 10 x 10GB ~80 GB
Total Data Usage: ~2 TB (2071 GB)

SFGF Storage Policy

Total online storage capacity at SFGF is limited, so it is important to transfer or arrange for delivery of your data as soon as possible after your run is complete.   There is no provision for long-term storage at this time.  Data will be retained a sufficient time for you to examine and accept base call data derived from images and to arrange for the delivery or download of your data.  If your data is delivered by disk, SFGF will retain the original data for a minimum of one week after disk delivery so that you may verify the contents and accessibility of the data from your computer.  Once accepted, the backup and protection of your data becomes your responsibility.

Image data will be retained online for a minimum of one week and base call data will be retained for a minimum of one month for download or transfer to disk.  After these minimums, data may be migrated at SFGF’s discretion to external or offline storage at your expense (charges as listed above).  Data migrated due to the expiration of these periods will become the responsibility of the customer.    Please note, that for all but the fastest network connections, one week is insufficient time to download image data for large runs, and therefore, transfer to an external hard disk is recommended.

 

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