I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I map to reference with minimap2 it produces no contigs.
Is 25bp too small to be a reference? I can potentially extend it but it's right in an area of conservation in this region of a gene and I would rather not extend much farther.