Question: How to annotate peaks using gencode27?
0
gravatar for mr.monahton
2.0 years ago by
mr.monahton20
mr.monahton20 wrote:

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?

ADD COMMENTlink modified 2.0 years ago by Hussain Ather940 • written 2.0 years ago by mr.monahton20
2
gravatar for Hussain Ather
2.0 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

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

ADD COMMENTlink written 2.0 years ago by Hussain Ather940
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