Multiple Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Biologics/Antibody Design

  • Role-based/Bioinformatician

  • Role-based/Biologist

  • Product-based/AbXtract

Description

This floe will use the region of interest (ROI), grouped sample information, and selection round information to provide relative abundance and enrichment values over sequential selection rounds. Select all datasets whose sample names are contained in the enrichment table loaded below. Load one dataset per sample per selection round. This floe retains only one instance of each ROI per enrichment group, prioritizing that found in the latest selection round. The full length count corresponds only to that instance of the sequence.

Parameter title in user interface (promoted name)

  • Output CSV Filename (file_name) type: file_out: All records are written to downstream csv file, must contain the *.csv extension
    Default: enrich.csv

Parameter title in user interface (promoted name)

  • Failed Dataset Output Name (data_out) type: dataset_out: Contains failed records from both upstream and downstream Processes
    Default: problematic.enrich_floe

Parameter title in user interface (promoted name)

  • Enrichment Table (barcode_table) type: file_in: XLS/CSV/TSV file containing sample names in the format Name,round_enrich(e.g., 1, 2, 3, etc.),enrich_group

Do not include header. Rounds do not need to be sequential but must be numeric. They will be considered in numerical order with largest value considered the latest round. Only one sample per round per enrich_group. Name should match sample names from original barcode table. Each sample name can only be used once.

Parameter title in user interface (promoted name)

  • Keep Only Functional Sequences (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shifts
    Default: True

Parameter title in user interface (promoted name)

  • Metrics for Ranking (ranking_criteria) type: string: Place metrics in order of ranking
    Default: [‘Latest Selection Round Detected’, ‘Net Fold Enrichment’, ‘Last Round Relative Abundance’, ‘Last Round Count’]
    Choices: Latest Selection Round Detected, Last Round Count, Last Round Relative Abundance, Net Fold Enrichment

Parameter title in user interface (promoted name)

  • Region to Consider for Enrichment (roi) type: string: Indicate the region of interest that should be considered for the enrichment
    Default: CDR3 Chain 2
    Choices: Merged CDRs, CDR3 Chain 1, CDR3 Chain 2, HCDR3 and LCDR3, Full-Length

Parameter title in user interface (promoted name)

  • Output Name of Dataset with Enrichment Calculation (data_out) type: dataset_out: Dataset name of sequences with enrichment and percent ROI calculation
    Default: enrich