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find peaks over a set of genes

Hi everyone, I have a set of genes:

>  genes
    ENSMUSG00000000811
    ENSMUSG00000000812
    ENSMUSG00000000813

and a chip-seq bed file.

chr8    70797397    70797576
chr8    70804936    70805149
chr8    70833619    70833922
chr8    73225728    73225908

I would like to find the number of peaks in each gene in genes. can anyone help? best

chip-seq r rna-seq
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written by ta_awwad ta_awwad

In R, you could import the mouse gencode annotation .GTF file (like this one for m39 genome) to get a GRanges of the genes:

library(GenomicFeatures)
txdb <- makeTxDbFromGFF(file = "gencode.gtf", organism = "Mus musculus")
genes <- genes(txdb)

And then also import your ChIP-seq .BED file as a GRanges to finally use countOverlaps,findOverlaps to see and count the overlaps between the two.

• 0 views • link
written by Papyrus Papyrus

thank you so much for your answer. I did it already. I thought there is a package that can do it for me. thanks once again

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written by ta_awwad ta_awwad

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