DMR Analysis for RRBS: what annotation file to I use?

Question

[embueno]

Hi,

I’m interested in running a DMR analysis on RRBS data. I was wondering what type of annotation file I need for the program (i.e methylkit or others) to identify promoters vs introns etc. Would a gtf file be enough?

I work with a non model organism (Leptinotarsa decemlienata) so I’m having some trouble following package tutorials that annotate their results using other R based packages. I’m just getting started on this so I would appreciate any input I can get.

Thanks!

Answer 1

[Papyrus]

If you have a custom GTF for your model species, you could try importing it into R with GenomicFeatures::makeTxDbFromGFF or rtracklayer::import to create a TxDb object. You could then use this object to annotate your regions of interest, for example using the ChIPseeker::annotatePeak function from the well-known package ChIPseeker.

Another package which has options for custom annotations is annotatr.

[Ming Tommy Tang]

once you have the txdb object , you can follow this to get the promoters and others