Overlap Among Different Datasets - AbXtract¶
Insert all the datasets from different source populations (e.g., barcode group) and the region of interest (ROI) and the FLOE will create an overlap_population field that indicates all of the populations to which a given ROI is found. One can use the ‘Modify the Sample Name/Barcode Group’ FLOE. May also specify a relaxed stringency for the overlap among populations by increasing the edit distance for given Levenshtein distance or Hamming distance method.
- Select All Overlay Datasets (data_source) : Inputs All the datasets (must be multiple datasets) by a given region of interest (ROI) NOTE: If file does not contain a sample_name or it is unknown, will use the dataset name.
- Region of Interest (ROI) For Condensing Sequences (string) : This will condense the SANGER sequences based on the ROI based rank ordered on abundance. All values sharing same ROI will display concatenated ‘:’ separated list by the ‘id’ field. IMPORTANT: all redundant sequences ROIs will be removed if lower abundance. If two sequences have same count by ROI only one will be selected at random. Default values condense by full-length including framework regions.Default: Full-Length, Including FrameworkChoices: Merged CDRs, CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3, Full-Length, Including Framework
- Edit Distance For Overlap By ROI Of Different Barcode Groups (integer) : If there are multiple downstream barcode groups, these will be compared to one another.Default: 300 Min: 1 Max: 1000000
- Edit Distance Method For Overlap Among Different Barcode Groups (string) : Indicate the type of edit distance method to apply for the overlap to complete population. NOTE: Only in effect if edit distance does not equal 0.Default: Levenshtein DistanceChoices: Levenshtein Distance, Hamming Distance
- Region Of Interest For The Overlap (string) : Species reference database to generate the db for igmatcher.Default: CDR3 Chain_2 (Downstream Chain)Choices: Merged CDRs, CDR3 Chain_1 (Upstream Chain), CDR3 Chain_2 (Downstream Chain), HCDR3 and LCDR3, Full-Length, Including Framework