Question: error in rGADEM
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gravatar for saumya2sarkar2
5 months ago by
saumya2sarkar20 wrote:

path1<-system.file("/home/sandeep/Desktop/Saumya/Chip 1st exp/peakbed/H3K4_Input_peaks.bed",package="rGADEM") pwd1<-"/home/sandeep/Desktop/Saumya/Chip 1st exp/peakbed/H3K4_Input_peaks.bed" BedFile1<-paste(pwd1,path1,sep="") BED1<-read.table(BedFile1,header=FALSE,sep="\t") BED1<-data.frame(chr=as.factor(BED1[,1]),start=as.numeric(BED1[,2]),end=as.numeric(BED1[,3])) rgBED1<-IRanges(start=BED1[,2],end=BED1[,3]) Sequences1<-RangedData(rgBED1,space=BED1[,1]) library("BSgenome.Rnorvegicus.UCSC.rn6", lib.loc="~/R/x86_64-pc-linux-gnu-library/3.5") gadem1<-GADEM(Sequences1,verbose=1,genome=Rnorvegicus) Retrieving sequences... Error in .getOneSeqFromBSgenomeMultipleSequences(x, names[i], start[i], : sequence 1 not found

chip-seq • 155 views
ADD COMMENTlink written 5 months ago by saumya2sarkar20
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