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ChipSeeker genomic features

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
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updated by Biostar Biostar • written by GK1610 GK1610

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)

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written by Santosh Anand Santosh Anand

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

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written by GK1610 GK1610

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

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written by Santosh Anand Santosh Anand

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