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5 months ago
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I have a .gfa file (e.g. "hprc-v1.0-pggb.gfa") corresponding to a pangenome reference, and assorted associated other files. I want to look up which nodes correspond to a particular gene, e.g., the amylase gene on chr1 which is at 103,655,760-103,664,554 on hg38. How do I figure out which pangenome nodes this corresponds to in my .gfa file?
Alternatively, is there a single example anywhere of a coordinate (or gene) to node mapping? E.g., something which says "the amylase corresponds to nodes 1000, 1001, 1002, and 1200 in the pangenome reference XYZ."