st3@k to_go
Member
- Joined
- Jun 26, 2025
- Messages
- 5
My buddy just started using HISAT-3N for some of his DNA analysis, specifically for a special BSseq experiment.
He's gotten the conversion table from it, which shows him how many bits changed and how many didn't at different spots.
Now, he's trying to figure out if he can tell the "context" of those changes, basically, if it's a CG, CHG, or CHH type of methylation.
He saw that you can tell HISAT-3N to only look for CGs, but he needs all of them. You know, other programs, like Bismark, just give you this info automatically.
The thing is, he's put a ton of work into setting up his whole process with HISAT-3N, so he really doesn't want to ditch it and start over with something else.
Does anyone know if there's a way to get that CG, CHG, or CHH info using what he's already got from HISAT-3N? Any help would be awesome!
He's gotten the conversion table from it, which shows him how many bits changed and how many didn't at different spots.
Now, he's trying to figure out if he can tell the "context" of those changes, basically, if it's a CG, CHG, or CHH type of methylation.
He saw that you can tell HISAT-3N to only look for CGs, but he needs all of them. You know, other programs, like Bismark, just give you this info automatically.
The thing is, he's put a ton of work into setting up his whole process with HISAT-3N, so he really doesn't want to ditch it and start over with something else.
Does anyone know if there's a way to get that CG, CHG, or CHH info using what he's already got from HISAT-3N? Any help would be awesome!
