I mapped the reads with the reference fasta with minimap2. Out put: BAM file
Then I used the BAM, reference fasta, reads to nanopolish variant calling. And I got this error.
Error: genome has multiple contigs, please use -w to specify input region
My reference fasta contains 6 fasta sequences. It has no chromosome locations in it. Without knowing the chromosome locations (format: <chromsome_name>:<start>-<end>)) how do I specify the input region?