Entering edit mode
I have file with 3 columns
Chr start end
I read it to Granges object :
Data <- read.table("file",header=T)
#create Granges object
object <- GRanges(seqnames=Rle(Data$Chr),ranges=IRanges(Data$start,end=Data$end),seqlengths=c(chr1=249250621,chr2=243199373,chr3=198022430,chr4=191154276))
I have two questions:
Q1-How it is recognized that at this position the nucleotide is G or A even if no information about reference genome is provided (nothing determine if it is human or mouse genome for example or it can be known from chr. length).
Q2-if I have the reference sequence in fastq format and i would like to read data into granges object whereas reference genome is the fastq file ,how to do that?
Re Q1, where have you seen any indications about sequence information? Here is what I have, based on the code you provided:
> library("GenomicRanges") > Data = data.frame(Chr = paste0("chr", 1:4), start = 1000001:1000004, end = 2000001:2000004) > Data Chr start end 1 chr1 1000001 2000001 2 chr2 1000002 2000002 3 chr3 1000003 2000003 4 chr4 1000004 2000004 > object <- GRanges(seqnames=Rle(Data$Chr), ranges=IRanges(Data$start,end=Data$end), seqlengths=c(chr1=249250621,chr2=243199373, chr3=198022430,chr4=191154276)) > object GRanges with 4 ranges and 0 metadata columns: seqnames ranges strand [1] chr1 [1000001, 2000001] * [2] chr2 [1000002, 2000002] * [3] chr3 [1000003, 2000003] * [4] chr4 [1000004, 2000004] * --- seqlengths: chr1 chr2 chr3 chr4 249250621 243199373 198022430 191154276Dear Asma, just wanted to let you know that I update some formatting to differentiate between
code chunksand text to increase the readability. Best wishes, Laurent