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How to annotate peaks using gencode27?

Hi guys, I'm trying to use ChIPseeker to annotate my peaks. I have used TxDb.Hsapiens.UCSC.hg38.knownGene as transcript database, but due to some issues I want also to annotate my peaks in reference to gencode27 database. I tried downloading gff file of basic annotation from Gencode and when I perform annotatePeak function from ChIPseeker package in R, all the peaks are annotated as "Promoter (<=1kb)" and many entrezID are missing when I use annoDB=org.Hs.eg.db Can anybody help me please with this?

chip-seq annotation chipseeker r gencode
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updated by Hussain Ather Hussain Ather • written by mr.monahton • mr.monahton

1 answer

You could try using another software like IGV to visualize your data and use the Region Navigator to annotate peaks.

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written by Hussain Ather Hussain Ather

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