Find genes neighboring to gene of interest

Question

[poojasethiya]

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

[Alex Reynolds]

There are lots of answers on this question already on Biostars. Search for "closest-features" and look at the --closest and --dist options.

Answer 1

[EagleEye]

BEDtool closest

[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.

[EagleEye]

Hi poojasethiya,

It is not the same. Please read the manual carefully before concluding. In bedtools closest, you can get first gene hit to your reference list by using '-t first'. And for upstream and downstream you can choose '-fu' and '-fd' respectively.

Answer 2

[Kristoffer Vitting-Seerup]

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