need clarifications on the workflow

PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data

BSD 3-Clause Clear License

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need clarifications on the workflow #58

Closed splaisan closed 1 year ago

splaisan commented 1 year ago

Dear all,

I am not sure I understood all the details of this pipeline. I have HiFi reads from a SequelIIe from a run with kinetics ON Is it correct that I need to run:

jasmine on my original SMRT-LINK HiFi reads with kinetic info (m123456e_230922_123124.hifi_reads.bam )
pbmm2 align (with --sort) of the resulting jasmine BAM reads against the reference genome
aligned_bam_to_cpg_scores on the pbmm2 sorted BAM mappings

Please correct me if I misunderstood!

Thanks in advance Stephane

ctsa commented 1 year ago

Hi @splaisan - Sorry for the delay, yes that is the correct workflow starting from a bam file with kinetics.