ChipSeeker genomic features

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7.7 years ago

GK1610 ▴ 120

Hi

Does anyone know how promoters, introns, exons , 5utr, 3utr, downstream and distal intergenic regions are quantified or determined for a given set of peak in ChIPseeker package

https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

ChIP-Seq • 2.6k views

ADD COMMENT • link updated 7.6 years ago by Biostar 20 • written 7.7 years ago by GK1610 ▴ 120

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It is using annotation from R annotation package TxDb.Hsapiens.UCSC.hg19.knownGene , which in turn is based on knownGene of UCSC table ( check uscs table browser and you should get the same annotation)

ADD REPLY • link 7.7 years ago by Santosh Anand 5.8k

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Thanks, do you know how it does for distal-intergenic region?I couldn't find that

ADD REPLY • link 7.7 years ago by GK1610 ▴ 120

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My guess will be that it is far from TSS (>3k) of gene. But why do you need this info?

ADD REPLY • link 7.7 years ago by Santosh Anand 5.8k

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