Let me explain: I want to use a small "reference genome" of only a gene, for use in examples. But I need it to still have the coordinates that correspond to the actual genome coordinates. But when I create a
GmapGenome using this truncated fasta, it begins at index 1, which prevents me from using it as wanted.
The header of the fasta file:
>18 dna:chromosome chromosome:GRCz11:18:5213338:5227420:1
This is how I build the genome:
refGenome <- gmapR::GmapGenome('slc24a5.fa', create=TRUE)
I want to be able to reference the genome using coordinates between 5213338 and 5227420, instead of 1 and 14083 (the length of the gene). Is this possible?
To clarify, what I need to do in the end is call variants (with VariantTools) using BAM files (aligned to genomic coordinates).