Downloading Data

How to download data, along with how to search and discover the data files that are available

This page overviews how to find what data files exist, along with how to download the data files via SFTP, and eventually, hopefully using globus.

1. Head to NExtSEEK and log in with your NExtSEEK/SEEK credentials

2. Head to the Data Query/Advanced Search

3. This is a broad text search of the entire database. Search any term/sets of terms to filter down and find the samples you want. For example, if you are interested in all sequencing files, you could search the sequencing sample type name, D.SEQ

Advanced search page. The "Search Value" box is a raw text search of the entire database. Allows optional sample type filtering along with simple search logic (AND/OR/NOT). The "Current Query Box" is also directly editable as well.

1. There are two ways to view the data:

   1. To view a single sample -> click on the value of the ID column.

      The sample page has an interactive sample tree on top that contains all associated sample types of that sample (children and parents), along with the specific metadata for that sample in tabular format below

   2. To view many samples, select the checkbox (as shown below) and download the samples. This downloads an excel file with all associated sample types in separate sheets.

Downloading samples

Each sample type is a different sheet. Samples are linked via UID and Parent Columns. D.SEQ-240422BTC-1 is connected to DNA-240422BTC-24. If you are interested in that DNA sample, check the DNA tab and look for the metadata surrounding that sample.

1. You can copy and paste the values that exist in the Link_PrimaryData into your filesystem (cloud or local) to download these files. Replace the username and password with the SFTP username and password associated with your account.

1. To run multiple get commands with only one login, follow this protocol

   • Create a text file (batch in the below example), and paste all of the get commands in there

     • get filename . -> replace filename with the name of the file (as in the SEEK metadata), and the . places the file in the directory you are running the SFTP command from

   • Then run the below command, and type your password in after. This will then iteratively run all of the get commands in the file "batch"

sftp [e-mail]:public < batch
## where username = your username, batch = the text file with the get command
## as shown in the example below

Example of how to batch download files.

For any assistance with SFTP: [e-mail]