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).
Ok, in my case, I want to call variants in this region, but the BAM files are in genomic coordinates. If I understand right,
mapToTranscripts()would help if I had the BAM files in transcript coordinates, called variants, and then converted to genomic coordinates. Is that right, and if so, is that the only way?Sorry, I meant
mapFromTranscripts. You could call variants in your restricted genome space and then map to the true genome using that function.Ok. That won't exactly work for what I wanted to do, since I wanted to have the BAM files and genome all ready to plug into a pipeline of which variant calling is only a part, but thank you for the response!