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Visualizing 5mC/5hmC at only CG or CH sequence. #1479
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Basemod visulaization does not depend on context (CG or CH). I'm not really sure what you are asking for, IGV is going to display base mods chosen wherever they appear. |
There are options in current IGV at "Color alignments by" -> "bisulfite mode" -> "CG" for whole-genome bisulfite sequencing data. |
OK, I understand I think. Your language is fine, I think the title of the ticket summarizes it well. To generalize this, If I understand correctly, you are requesting that base modifications be shown only at specific contexts. By that I mean only at genomic locations that contain a specific sequence. I can see how that might be useful but it would be complex to implement, and I cannot see this being prioritized anytime soon. |
Yes! That is exactly what I meant. |
Let's leave it open for now, I'm just trying to be realistic about the effort and time. @marcus1487 @ctsa do you have any thoughts on this? |
@miwi610 Have you tried the single color option |
Dorado basecaller for ONT can call 5mC/5hmC not only at CpG, but also at CH sequence, now.
And many researchers, I think, like to visualize the modification at CG and CH separately, as IGV have those options at bisulfide mode.
If there are not so yet, please implement to visualize 5mC/5hmC modification of ONT bam at CG and CH sequence, separately, similar to bisulfite mode. I checked the newest 2.17.1 and could not find such option so far.
I am not sure if there are needs for 6mA modificaiton at only AT and A[C|G|A], too.
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