Dear all,
Let me start saying that I'm quite a newbie in processing genomic data since I have a different background, so I apologize for maybe too simple questions:
I have populations.snps file in .vcf format which I would like to visualize on vcfR.
I'm following the vcfR manual and it has been said that in order to visualize the data I need to create a chromR object first. This chromR is composed by my vcf file, a fasta file (which I suppose to be my reference genome), and a gff file. Example below:
Input the files.
vcf <- read.vcfR(vcf_file, verbose = FALSE) dna <- ape::read.dna(dna_file, format = "fasta") gff <- read.table(gff_file, sep="\t", quote="")
Create a chromR object.
chrom <- create.chromR(name="Supercontig", vcf=vcf, seq=dna, ann=gff, verbose=TRUE)
So, I have my vcf file and fasta file, but I miss the gff one. When I downloaded the reference genome before performing the alignment, together with the Fasta file, I got different formats files (.ann, .amb, .bwt, .pac, .sa) but any of those was in a gff format. I wonder where I should get this format type, or if I can use one of those I got (like .ann file?) to create a chromR object.
I don't know if this is helpful, but the reference genome was: Gasterosteus_aculeatus.BROADS1.dna.toplevel.fa
Looking forward to hear a feedback,
cheers,
Gio
