Entering edit mode
the Error is when i want to load bed file with using "readTranscriptFeatures" in Genomation R package
feats = readTranscriptFeatures("gff_assembly_to_bed.bed") Reading the table... Calculating intron coordinates... Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 1: 'end' must be >= 'start' - 1.
i checked the bed file there is not values for end greater than start? Anybody know how i can find whats the error?
thanks
sat
Is the bed file publicly available? If so you might point to where others could get it.
Hi James, thank you. no. unfortunately, this bed file im using it is not publicly available.
OK. Without either the example data or a self-contained example I am afraid it is unlikely that anybody can help. But do note that the error comes from calculating the intron coordinates, which may indicate that there are genes where the start of one exon is smaller than the end of the preceding exon (but the exons themselves have starts < ends), in which case the intron between those exons might be inferred to have a start > end. So you might check for that.