bcgsc
Support/distinction of other linked-read technologies
Hello, I'm interested in incorporating this tool into Harpy, which is specific to haplotagging-style linked reads. The documentation provides the option for 10x and stFLR protocol types, but not other varieties like haplotagging or TELLseq.
My question is: is there an appreciable difference of what the two protocols alter within physlr and would it be possible to add support for haplotagging-style barcodes? The haplotagging barcodes are still provided in the BX:Z tag, but are in the format AxxCxxBxxDxx where each xx is an integer between 0-99 e.g. A02C96B34D51.
Sort of related to that, is that deconvolved barcodes may feature a hyphenated ending (e.g. BX:Z:<barcode>-1) or an additional MI:i: tag of a simple integer indicating the unique molecule those barcodes are said to be associated with (e.g. MI:i:41 and MI:i94122). Is there value in prioritizing the MI:i tag, if present, over the BX:Z tag?
