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5mC coloring mode

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Jim Robinson edited this page Aug 9, 2022 · 13 revisions

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

This coloring scheme is designed to create visualizations of alignments with modified bases specified with MM and ML tags (see the Sam Tags specification) that are consistent with the color scheme for bisulfite sequencing experiments. While designed for consistency with prior visualizations of methylation data, it can be used with any modification, not just 5mC. 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 modifiations with probility > 50% are colored red

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

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