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!
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written
by
embueno •
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.
once you have the txdb object , you can follow this to get the promoters and others
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