I want to find genes upstream and downstream to gene of my interest based upon the chromosomal co-ordinates. I tried using precede, follow from GRanges package but it does not report the genes which have overlapping co-ordinates (for small genome size, genes are placed very close). How can I get the immediate first neighbor/closest to start and end of my gene.
~Pooja
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poojasethiya
BEDTools closest is same as GRanges findOverlap and it just give overlapping genes but not the preceding/succeeding genes. I want very first neighbor it can be overlapping, preceding and succeeding. Is there any way I can get the nearest.
Alternatively you can just reduce all the gene to the transcription start site (or other point of interest) and then use GRanges with the approach you suggest
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There are lots of answers on this question already on Biostars. Search for "closest-features" and look at the
--closestand--distoptions.