Enrichment and Depletion Tracing of Clones¶
Calculates the relative fold enrichment over multiple rounds of selection in the context of a given region of interest. The number of records in the output is geared to identify the final round in the context of earlier rounds. This is to avoid redundancy in the final output. So, if values are found in multiple rounds, the latest round copy of the full-length sequence is retained and the sequence region-of-interest is given a minimal frequency in any subsequent rounds if they exist. Note that sequences not belonging to samples in the Enrichment Table are excluded from the output.
Main Parameters¶
Parameter Name |
---|
Enrichment Table |
Correction Factor Group 1 |
Correction Factor Group 2 |
Keep Only Functional Sequences |
Metrics for Ranking |
Region to Consider for Enrichment |
Minimum Count for the Region of Interest (ROI) |
Minimum Percent for the Region of Interest (ROI) |
Write the Enrich and Relative Abundance Output to CSV File |
Parameter Details¶
Calculation Parameters¶
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.
Correction Factor Group 1 (correction_factor1) type: integer: Final round clones not found in earlier rounds are given pseudocount equal to minimum of early round count divided by this value; larger value means greater weight to clones found only in final round.Default: 2 Correction Factor Group 2 (correction_factor2) type: integer: Early round clones not found in final round are given pseudocount equal to minimum of final round count divided by this value; larger value means bigger penalty for de-enrichmentDefault: 10 CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128 Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592 Keep Only Functional Sequences (filter_functional) type: boolean: Eliminates non-functional sequences, truncations, stop-codons, frame-shiftsDefault: True None (floe_report_name) type: string:Default: Trace Enriched Populations GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16 Input dataset CSV files (input_csv) type: file_in: Input annotated data in CSV format from upstream AbXtract floes. Accepts multiple inputs. Required for high-diversity datasets >50,000 total records. Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “” Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592 Metric Period (metric_period) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300 Metrics for Ranking (ranking_criteria) type: string: Place metrics in order of rankingDefault: [‘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 Region to Consider for Enrichment (roi) type: string: Indicate the region of interest that should be considered for the enrichmentDefault: CDR3 Chain 2Choices: Merged CDRs, CDR3 Chain 1, CDR3 Chain 2, HCDR3 and LCDR3, Full-Length Minimum Count for the Region of Interest (ROI) (roi_count) type: integer: This will set the minimum count for a given region of interest, all below will be removed. Only applied to the final round. Be aware that clones not present in final round will have pseudocount values often <1. These will be retained if minimum count is set to 1 or 0.Default: 1 , Max: 10000000000 Minimum Percent for the Region of Interest (ROI) (roi_percent) type: decimal: This will set the minimum percent for a given region of interest, all below will be removed. Only applied to the final round. Be aware that clones not present in final round will have pseudocount values below the minimum percent for true clones.Default: 1e-12 , Min: 1e-12, Max: 100 Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64 Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required Write the Enrich and Relative Abundance Output to CSV File (write_to_csv_file) type: boolean: Allows the option to write to CSV after the AbXtract Processing file at the cost of additional time. If not, can do this in separate step. Writes to empty file if turned off.Default: True
Hardware Parameters¶
- Machine hardware requirements
- Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 1800 , Min: 256.0, Max: 8589934592
- Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64
- Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.Default: 5120.0 , Min: 128.0, Max: 8589934592
- GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16
- CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128
- Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
- Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
- Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)Default: “”
Metrics Parameters¶
- Cube Metric Parameters
- Metric Period (None) type: decimal: How often to sample metrics, in secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
- Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network