Logomaker for Antibody CDRs - AbXtractΒΆ

This FLOE will produce sequence logos by region of interest (ROI) and output to FLOE REPORT.

Promoted Parameters

  • Processed RECORDS, Long-Read or Single-Chain (data_source) : The dataset(s) to read records from.
  • Analyzed Report Name (dataset_out) : Floe report to write to.
    Default: Seq_Logo
  • ROI for sequence logo (choose Chain1 CDR3 if short-read/single-chain data) (string) : Name of regions to be aligned for sequence logo. Logo is output only if not more than 500 records.
    Default: CDR3 Chain_2 (Downstream Chain)
    Choices: CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3
  • Split by cluster? Only applies to downstream records. (boolean) : Indicates whether to split sequences by cluster before creating sequence logos. Cluster logos are output only if not more than 500 records.
    Default: False

Hidden Parameters

  • Metrics to Assess Sanger in Presence of NGS (boolean) : Indicates whether additional metrics are to be included to identify Sanger sequences in NGS and vice-versa.
    Default: False
  • Are these already processed records? (boolean) : Indicates whether input is to be analyzed post-processing for generating specific plots.
    Default: True
  • Is This A Downstream Processed File? (boolean) : Indicates whether the input contains data for downstream processing.
    Default: False
  • Is This A Sanger Processed File? (boolean) : Indicates whether the input contains Sanger (low-throughput) Sequencing Data.
    Default: False
  • Write Records to Dataset (boolean) : Write out a records to dataset.
    Default: False
  • Write Group to Their Own Dataset After Processing (boolean) : Write group (if provided) to their own dataset after processing. NOTE: if only a single group then no separate dataset will be written.
    Default: True
  • Write Report (boolean) : Write out a floe report after consolidation.
    Default: True