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Question: [ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in gene A & defined TSS region of gene B)
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gravatar for chiefcat
2.8 years ago by
chiefcat • 150
chiefcat • 150 wrote:

Hi guys,

I'm trying to use ChIPseeker but couldn't find a way to call the overlapping features during peak annotation.

Example:

TSS setting: -3kb +500bp

--> I would like to get the ChIP peak annotated with "Rrs1, 3'UTR" & "Adhfe1, TSS" I've tried a lot of different arguments but all of them just me ONLY "Rrs1, 3'UTR" enter image description here

Do anyone know how to do this?

And If a peak is overlapping with 2 different gene promoters, can ChIPseek annotate this?

Thanks!!
chip-seq chipseeker annotation • 1.8k views
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modified 2.8 years ago by Guangchuang Yu • 2.3k • written 2.8 years ago by chiefcat • 150
0
gravatar for Guangchuang Yu
2.8 years ago by
Guangchuang Yu • 2.3k
China/Guangzhou/Southern Medical University
Guangchuang Yu • 2.3k wrote:

there is a genomicAnnotationPriority parameter documented in https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#peak-annotation. You can select to report "Rrs1, 3'UTR" OR "Adhfe1, TSS", but and "Rrs1, 3'UTR" & "Adhfe1, TSS" as annotatePeak only report the 1st hit according to the annotation priority.

Maybe setting the parameter addFlankGeneInfo = TRUE, flankDistance = 1000 will give you some useful information. The above parameters will report a new column of flanking genes with all the genes at the flanking region of the peak (e.g. [-1000, 1000] if flankDistance = 1000).

ADD COMMENT • link written 2.8 years ago by Guangchuang Yu • 2.3k
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