Extract features file

[yycunc]

Dear, I align the ccs.bam to genome using ccsmeth align and the output is input into ccsmeth extract as follows. But I get empty file and without any error stdout.

[PengNi]

Hi @yycunc , the log shows that all reads are skipped/failed. What is the type (SequelII or Revio) of your ccs.bam? Are there kinetics signals for the reads in the hifi.bam (i.e., are there fi, fp, ri, rp, fn, rn tags in each segment in the bam file)?

[zeruiWang]

Hi @yycunc , the log shows that all reads are skipped/failed. What is the type (SequelII or Revio) of your ccs.bam? Are there kinetics signals for the reads in the hifi.bam (i.e., are there fi, fp, ri, rp, fn, rn tags in each segment in the bam file)?

作者您好，我也碰到了相同的问题，revio数据的kinetics signals的被jasmine(https://github.com/pacificbiosciences/jasmine/) 处理后没有了fi, fp, ri, rp, fn, rn tags。我是否可以使用pbtk (https://github.com/PacificBiosciences/pbtk) 的ccs-kinetics-bystrandify（Converts a PacBio BAM or DataSet XML file containing CCS kinetics tags to a pseudo-bystrand file with pw and ip tags that can be used as a substitute for subreads in applications expecting such kinetics information）来处理呢？

（https://github.com/PacificBiosciences/kineticsTools/issues/95） 这个问题似乎与ccsmeth在处理revio数据上碰到的这个问题类似，希望您能指导一下