search

PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
62 stars 5 forks source link

cannot get 5mc probability Revio platform #65

Closed Duyh814 closed 4 months ago

Duyh814 commented 6 months ago

Hey i 'm now trying to call 5mc probability from Pacbio revio ccs.bam, but i failed. i find the hifi-kinetic signal in revio ccs.bam, but i can not use pbmm2 map the methyaltion signal to reference genome, which is different from pacbio seqII platform. Is there anyway to call the 5mc probability from pacbio revio platform

ctsa commented 6 months ago

Hi @Duyh814, You can use Jasmine (https://github.com/PacificBiosciences/jasmine) to first process the kinetic signal into 5mC probabilities, then map with pbmm2. After mapping pb-CpG-tools can be used to generate 5mC pileup tracks.

Duyh814 commented 6 months ago

Hi @Duyh814, You can use Jasmine (https://github.com/PacificBiosciences/jasmine) to first process the kinetic signal into 5mC probabilities, then map with pbmm2. After mapping pb-CpG-tools can be used to generate 5mC pileup tracks.

Thank you, I appreciate it.

Duyh814 commented 6 months ago

@ctsa Hi ，Is this software a replacement for primrose? I‘m not sure if their having same function

ctsa commented 6 months ago

Yes jasmine is the replacement for primrose.