Annotate peaks and G quadruplex

Question

[ab2063]

I am a beginner in R. I have ChIP peaks and G quadruplex hg19 data. I want to annotate these peaks with G quadruplex, in addition to conventional features like promoter, intron, exons etc. in feature distribution plot. Any suggestions on packages that I can use to annotate the peaks.

[manaswwm]

When I was a beginner in R I used QuasR - tutorial for this : https://bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html. This I found extremely helpful for annotating peaks and features, this tutorial also introduces to other packages which are helpful ex : Gviz - tutorial link : https://www.bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html

[ab2063]

Thank you for the links

Answer 1

[gdaly9000]

Are both your files bed (that is interval) formatted? If so you could use bedtools intersect, bedtools jaccard, bedtools reldist to see if they are correlated.

[ab2063]

Yes the files are Granges object. But as I said I am a beginner and not yet comfortable using command lines and BEDtools. Is there a way to do it in RStudio.

Answer 2

[Rongxin]

Hi, for the beginner of R, I recommend the Bioconductor package ChIPseeker to you, which can help you to annotate the bed files and plot the distribution mode elements around G4s.