Hello,
I have a list of genomic coordinates from differentially methylation regions and a I need to extract from them a list of genes, and I don't want do look one region by one.
Is there a R package or other bioinformatic tool that can help me?
Thank you!
Hi, your genomic coordinates should be in BED format and you can get a list of genes for your organism in GFF or GTF format, so you can use bedtools intersect (https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html) to find the genes that overlap your differentially methylated regions.
hi
an other way for button pushing people would be in UCSC to construct a custon track and by the table browser choosing UCSC gene as base, get the genes.
fred
Hi Jaqueline,
you could try to use the bimoaRt package in R. You can easily extract gene names within individual regions by inputting start, end, and chromosome of your chromosomal region of interest.
The following code* will be helpful for individual regions of interest:
library(biomaRt)
mart
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