ChIP-seq peak annotation to gene in ChIPseeker
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@gyan-prakash-mishra-8555
Last seen 3 days ago
INDIA

Hi,

I am using ChIPseeker to annotate TF ChIP-seq peaks to gene. As mentioned in the article and tutorial, maximum distance cut-off can be used to annotate the peaks in annotatePeak function. I guesstssRegion is the option that can be used for max distance cut-off. tssRegion cut-off would be helpful as reasoned

binding sites might be located between two start sites of different genes or hit different genes which have the same TSS location in the genome.

However it is not clear to what is the maximal distance cut-off for a peak to be assigned to a gene, or all peaks forced to be assigned to the closest gene even if the distance is too long?

Thanks

Gyan

ChIPseeker • 137 views
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After going through the package, I think all the peaks are annotated to genes irrespective of distance to TSS. There is also another function dropAnno which can be used to filter out peaks based on its relative distance to TSS. Peak can also be filtered using normal dplyr::filter if output of annotaePeak is already converted to a data frame.

dropAnno(csAnno, distanceToTSS_cutoff = 10000)
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