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  • .bed file to GRanges object

    Hi,

    I have a bed file containing chromosome number and start to end position of reads. This bed file is 0-based so the first read starts from 0 instead of one.

    I converted the bed file into GRanges object in the following way:

    Code:
    makeGRangesFromDataFrame(mybedfile, starts.in.df.are.0based=T,
             seqinfo = Seqinfo(seqnames=as.character(unique(mybedfile$chr)),
    	 seqlengths = seq.lengths))
    I end up with a GRanges object of my bed file where the starting positions are all shifted by one nucleotide i.e. 0 become 1, 5 becomes 6, and so on. However, the end position is not shifted. It seems to me that the function trims one nucleotide of every read at the starting point. So, can anyone explain to me what is actually happen and what was the motivation?

    Thanks. Cheers.

  • #2
    The end doesn't have to be shifted. Obased bed files were done to make easier the calculation of the length of an interval. For example, if your read goes from bp number 2 to bp number 10 (a short read ), the length of your read is 9bp. With a 0based bed, this read will be annotated as going from 1 to 10 (so if you do 10-1=9 you directly get the length of the read), even though your read is not overlapping the nucleotide 1. Hope I'm clear enough...
    Last edited by SylvainL; 06-04-2015, 01:11 AM.

    Comment


    • #3
      Hey SylvainL. Thanks a lot for the explanation. They're clear enough so don't worry.. :-)

      Cheers.

      Comment

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