Calling methylation for small plasmids

[KuroRiposte]

Hi, was just wondering if call methylation would work for small sized plasmids (<10kb)? It seems that I can’t get any motif to show up (not even GATC, which is as expected in a dam+ Ecoli strain), while tuning modkit’s motif search shows the GATC motif.

[alexcritschristoph]

Hey, not entirely surprised by this! MicrobeMod really expects an entire genome to have enough examples of the motif present. Glad that modkit's new motif search catches them though. When we've had small plasmids we've just looked at the methylated sites in the MicrobeMod sites.tsv file by hand.