User: lifeng.liu.biology

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Posts by lifeng.liu.biology

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how to define the downstream range in ChIPseeker
... Does anyone know how to set the downstream range for the peak annotation? It seems the default setting of downstream is 3kb. I would like to set the downstream range from 3kb to 500bp. Thanks ...
chipseq chipseeker h3k27me3 written 10 months ago by lifeng.liu.biology10 • updated 10 months ago by Guangchuang Yu1.0k
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Answer: A: ChIPseeker peak annotation tssRegion
... Figured it out. The problem is the priority of the genomic annotation. Using the priority of ​genomicAnnotationPriority = c( "5UTR",  "Exon", "Intron", "3UTR", "Promoter", "Downstream","Intergenic") gives me same result with tssRegion=c(-3000, 3000)​ or tssRegion=c(-2000, 0)​. But if I change it to  ...
written 10 months ago by lifeng.liu.biology10
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Comment: C: ChIPseeker peak annotation tssRegion
... R script used here: library(GenomicFeatures) library(ChIPseeker) library(clusterProfiler) txdb <- loadDb("Bdistachyon_v314.sqlite") file_H3K27me3="H3K27me3_DiffBind_Peaks.bed" peak_H3K27me3 <- readPeakFile(file_H3K27me3) peakAnno <- annotatePeak(peak_H3K27me3, tssRegion=c(-3000, 3000), ...
written 10 months ago by lifeng.liu.biology10
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ChIPseeker peak annotation tssRegion
... I was confused about the argument of tssRegion in peak annotation function of ChIPseeker. It seems that there is no change of the annotation output when I changed the tssRegion setting, from tssRegion=c(-3000, 3000) to tssRegion=c(-2000, 0). I am working on a plant species, Brachypodium distachyon ( ...
chipseq annotation chipseeker written 10 months ago by lifeng.liu.biology10

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