Question

GRanges object from gene list

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rbronste ▴ 60

@rbronste-12189

Last seen 5.1 years ago

Wondering about the most straightforward way to take a list of genes and create a GRanges object, so basically pull the intervals for lets say a list of 500 RefSeq genes? Thanks!

granges bed genomicranges genomeintervals deseq2 • 1.6k views

ADD COMMENT • link 6.9 years ago rbronste ▴ 60

score 1 · Answer 1 · 2018-01-18

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

It depends on the source. For RefSeq in particular, you could use GenomicFeatures::makeTxDbFromUCSC() and ask for the "refGene" table (I think that's what it's called). Then, extract the desired features as a GRanges with e.g. genes(). There are probably resources available from AnnotationHub, as well.

ADD COMMENT • link 6.9 years ago Michael Lawrence ★ 11k

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That would we good for refSeq for sure, how would you approach it if just using official gene symbols, such as those in DESeq2 results()?

ADD REPLY • link 6.9 years ago rbronste ▴ 60

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You'll want to use whatever annotations were used to generate the counts.

ADD REPLY • link 6.9 years ago Michael Lawrence ★ 11k