Question: Chip-Seq peaks annotation
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gravatar for tarek.mohamed
3.5 years ago by
tarek.mohamed270
tarek.mohamed270 wrote:

Hi All, I am analyzing a chip seq data trying to identify DNA binding sites to a specific protein.I did the alignment using bwa, and peaks calling using macs2. Now I am using R package "chipseeker" to annotate these peaks. My question is how can I excluded micro-RNA encoding genes from the annotation. I would guess that I have to remove them from the txdb I used for annotating the peaks. Is there an easy way to do this?

library(ChIPseeker) library("TxDb.Hsapiens.UCSC.hg38.knownGene") txdb<-TxDb.Hsapiens.UCSC.hg38.knownGene peakAnnotation <- annotatePeak("narrowpeak_bowtie_q0.05_IgG.txt", tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

Thanks Tarek

chipseeker chip-seq • 1.9k views
ADD COMMENTlink written 3.5 years ago by tarek.mohamed270
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