I'm trying to find any programs or published scripts that can be used to systematically identify and return a list of genes within a specified distance of a response element.
I have a list of response elements identified via PoSSuM-search, which includes genomic coordinates for each match, and need to use this list and a .GFF3 annotation file to identify all genes that fall within XXkb (e.g 100kb) of those response elements.
Hi, Matthew Hale
I think you might find bedtools annotate (https://bedtools.readthedocs.io/en/latest/content/tools/annotate.html) useful for this kind of task.
Alternatively, the R package ChIPseeker has function called annotatePeak (https://www.rdocumentation.org/packages/ChIPseeker/versions/1.8.6/topics/annotatePeak) which you can use for this purpose. You might need however to make some formate tweaks. The functions takes a peak input (GRanges, in this case of your response elements and their coordinates) and a TxDb (which you can make from your GFF3 file using another R package called rtracklayer).
Hi Matthew Hale ,
If you have a list of genome coordinate (example., chr 2:12421-455677) you can use biomaRt package in R. Here, you do not need to GFF3 (but you must define species). because, it work by an online connection with ensemble database.
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