I would like to use the Gviz package but my I have a reference genome in FASTA format, not as a valid UCSC genome (it was not published yet).
It is possible to use this FASTA file instead?
Updated for @Florian:
Let´s say that I have one genome in FASTA format on disk:
library(Biostrings) ncrna <- readDNAStringSet(file = "GTgenome.fa") head(ncrna) A DNAStringSet instance of length 6 width seq names [1] 20202851 CCCAGTTTTCCCCACTCTGTGA...AAAGATCTTACAACCGATTTT chr10 Major... [2] 20315886 AGCCGACGAGACTCACAGAACC...TCACAAACCCCCTCGGGAGGG chr11 Major... [3] 20466350 GATTAGACCTCCGAAAGGGGTA...ATTATTAATTATTAAATATTA chr12 Major... [4] 16480340 GTCTCCACTTGCCCCACAACGG...AGATGACGATGATGAAGATGA chr13 Major... [5] 16193477 CTCTGTGACATCACAGCCATGG...GGGTTACACACGTTGTTTTTT chr14 Major...
Using the object created to replace a UCSC genome:
ideoTrack <- IdeogramTrack(genome=ncrna, chromosome="chr10", fontsize=14) Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 51 (char '3') not in lookup table In addition: Warning message: In if (!token %in% base::ls(env)) { : the condition has length > 1 and only the first element will be used
I am probably misunderstanding a very basic feature here, but I would be grateful for some help!
Florian, please check my update!
Florian, please check my update!