Skip to content

5mC coloring mode

Jump to bottom
jrobinso edited this page Jan 25, 2023 · 13 revisions

New coloring option Color alignments by > base modification (5mC)

This alignment coloring scheme was designed to provide visualization of 5-Methylcytosine (5mC) modifications specified with MM/ML tags that is consistent with visualization of methylation from bisulfite sequencing. In this scheme, color for modified bases is assigned based on the probability of the modification. Specifically:

  • Base modifications with probability < 50% are colored blue

  • Base modifications with probability > 50% are colored red

  • Alignments are colored to indicate strand

In both cases alpha transparency is applied, with the degree of transparency increasing as probability approaches 50%. So base modifications with probability 0% are solid blue, base modifications with probability of 100% solid red.

Example screenshots

Red bases indicate probability of 5-Methylcytosine (5mC) modification > 50%, blue indicate probability of 5mC modification < 50%.

Clone this wiki locally