Specimen Library Aliquot List

Overview

Generates a list of Library Aliquot NHash IDs from an overall specimen list retrieved from the Brain Knowledge Platform.

Retrieve Specimen Metadata from Brain Knowledge Platform

  • Step 1: Go to Brain Knowledge Platform

  • Step 2: Navigate to ‘Data/Projects’ tab on the top right menu

  • Step 3: Filter by ‘Specimen Type’ specifically “Library Aliquot”

  • Step 4: Click on specific project i.e. “BICAN Rapid Release Inventory: Single cell transcriptomics and epigenomics”

  • Step 5: Click on ‘BROWSE SPECIMENS’ button

  • Step 6: Click on download icon (arrow pointing down) on top menu bar and select ‘Metadata’

The input file manifest must be in CSV format.

Required columns:

  • Specimen ID

Optional columns:

  • Project ID

  • Library ALiquot NHash ID

  • Subject NHash ID

Command Line

bkbit list-library-aliquot

$ bkbit list-library-aliquot SPECIMEN_METADATA_CSV

Arguments

SPECIMEN_METADATA_CSV

Required argument

Examples

Example 1: Save list of library aliquots to file

# Run list-library-aliquot command
$ bkbit list-library-aliquot SpecimenMetadata.csv > library_aliquot_list.txt