Hello, everybody. When I was trying to use simulateSV of RSVsim to simulate the variants on the specific regions (defined by Granges) of chr8 from BSgenome.Hsapiens.UCSC.hg19. I have the error of "No regions on given chromosomes". The following is the code:

library("RSVSim")
library("GenomicFeatures")
library("BSgenome.Hsapiens.UCSC.hg19")

#for extracting 200 values in a random order. 
getdel_para <- function(par){
        set.seed(2546)
        sel <- unlist(floor(runif(200, 1, 800)))
        par.list <- c("list", 200)

        for(i in 1:200){
                sele <- sel[i]
                par.list[[i]] <- par[sel[i]]
        }

        return(par.list)
}

#getting chromosome 8 from genome.
genome <- BSgenome.Hsapiens.UCSC.hg19
gchr8 <- DNAStringSet(genome$chr8)
names(gchr8) = "Chr8"

#the "deletions.csv" is the file that records the deletion positions, size and deletion sequence name.
delfile <- paste("/paedwy/disk1/wma/simulate_CNV/chr_sv_data/fasta_collected/sample_", 1, "/deletions.csv", sep = "")
assign(delfile, rnorm(3)+5)
delget <- read.table(delfile, header = TRUE, sep="\t",stringsAsFactors=FALSE, quote="")

#get the start list and end list for the Granges.
start <- as.integer(getdel_para(delget$Start))
end <- as.integer(getdel_para(delget$End))
size.list <- as.integer(getdel_para(delget$Size))
delname <- getdel_para(delget$Name)
regions.list <- GRanges(IRanges(c(start), c(end)), seqnames=delname)

simSV <- simulateSV(output=NA, genome=gchr8, dels=200, sizeDels=c(as.integer(size.list)), regionsDels=regions.list, bpSeqSize=100)

#error log:
Breakpoints will be distributed uniformly across the genome
Error in simulateSV(genome = gchr8, dels = 200, sizeDels = c(as.integer(size.list)),  :
  No regions on given chromosomes

#P.S. The following is how does the regions.list look like:
> regions.list
GRanges object with 200 ranges and 0 metadata columns:
           seqnames              ranges strand
              <Rle>           <IRanges>  <Rle>
    [1] deletion349   15777396-15778345      *
    [2] deletion533   92473953-92480676      *
    [3] deletion420 137584332-137586099      *
    [4] deletion512 113994831-113998199      *
    [5] deletion658 115948646-115957703      *
    ...         ...                 ...    ...
  [196] deletion589   23523243-23534293      *
  [197] deletion138 108525154-108525886      *
  [198] deletion764   55632323-55658630      *
  [199] deletion278 143013155-143013817      *
  [200] deletion267   46843862-46844663      *
  -------
  seqinfo: 172 sequences from an unspecified genome; no seqlengths

Thanks

Hey,

The issue seems to be that the contig names (seqnames) in your regions.list object are not true contig names. Instead, you have assigned them as the IDs of the deletions via the following command:

regions.list <- GRanges(IRanges(c(start), c(end)), seqnames=delname)

seqnames should be, for example, 'chr8'. Take a look at the example HERE.

Kevin