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ZW-xjtlu / exomePeak2

Peak calling and differential methylation for MeRIP-Seq
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Usage of ExomePeak2 for Bacterial & Viral m6A #49

Open TaehyungKwon opened 3 months ago

TaehyungKwon commented 3 months ago

Hi,

I've been gratefully using ExomePeak2 for my m6A differential methylation analyses. Although I was focusing on eukaryotic hosts, I am interested in analyzing m6A in ssRNA & dsDNA viruses, and perhaps bacteria in future. May I ask your advice on parameters I should tweak for these cases? For example, I am using RNA-seq (& MeRIP-seq) reads that contain host and viral sequences.

Thanks, Taehyung

ZW-xjtlu commented 1 day ago

Dear Taeyung,

Sorry for the late reply on this important issue. ExomePeak2 currently does support virus genome m6A analysis. In this case, the challenge is that you need to supply a GTF file for the virus genome you want to analyze. I recommend that you set the entire virus genome as an exon in that GTF file (the GTF contains a single gene and single exon, which spans the virus genome you want to analyze). By doing so, ExomePeak2 can perform peak calling on a virus genome using default parameters.

Best wishes,
Zhen