Question: Filtering a BED file according to genomic annotation
gravatar for rbronste
11 months ago by
rbronste60 wrote:

I was wondering about a straightforward way to take a GRanges for instance that originate from a BED file and pull out intervals specific to different genomic features such as promoters or intronic/intergenic ChIP-seq peaks etc? Thanks. 

ADD COMMENTlink modified 11 months ago by Aaron Lun21k • written 11 months ago by rbronste60
gravatar for Aaron Lun
11 months ago by
Aaron Lun21k
Cambridge, United Kingdom
Aaron Lun21k wrote:

Just use findOverlaps to identify overlaps between your GRanges and the intervals returned by various functions from the GenomicFeatures package, e.g., promoters, exons, intronsByTranscript, and so on. You'll have to specify the transcriptome of interest, obviously, and you'll need to think about how to report the results when your regions overlap multiple features (e.g., intron/exon-spanning). But you would have to think about these things anyway, there's no obvious single answer for dealing with multiple overlaps.

Incidentally, csaw contains a detailRanges function that reports all overlaps of a set a genomic regions to common annotated features. However, this is mostly intended for reporting multiple overlaps in a compact tabular format, rather than for further analysis where some thought is required as discussed.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Aaron Lun21k
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