ipdSummary for Revio data

[jxmelody]

Dear,

Thank you for implementing this great tool.

I have a few questions about the applicability of Revio data. I am not very familiar with library preparation, but I was given metagenomic sequencing data (BAM file) generated by the Revio system. The analysis toolkit is SMRT Link 13.0.0.207600. The BAM file contains only HiFi reads as, from SMRT Link v11 onwards, subreads data is not generated.

Because I only have HiFi data, in order to use ipdSummary, I need to convert the HiFi data into pseudo subreads. I followed the steps in issue95. and successfully generated a subreads file.

My questions are:

1. Is the tool ipdSummary still applicable to my data? As I understand from the information on page 54 of the SMRT Tools Reference Guide v13.0.

   To simplify the process of finding DNA modifications with PacBio data, the tool includes a pre-trained lookup table mapping 12-mer DNA sequences to mean IPDs observed in C2 chemistry. If I am not mistaken, C2 chemistry is for the Sequel II system. Would it be inaccurate if I use ipdSummary directly for my data?

2. Could you please provide the training data used in ipdSummary, especially metagenomic sequencing data with kinetic information from the Revio system? I found a dataset from your FTP website , but I assume it is not WGA data.

Thank you for your assistance! Jin

[zek42]

Dear Hi jin, Recently, I have also been using the Pacbio Revio HIFI data to perform DNA methylation analysis on ipdsunmmy. I encountered this issue with the exception: Chemistry cannot be identified - cannot perform kinetic analysis. I followed issu99 and still encountered the same error. Have you resolved this problem? How was it resolved? Is it convenient to leave an email for communication? Thank you for your assistance! 曾 （zeka819@outlook.com）