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  • how to do methylation analysis using pacbio data

    I want to do methylation analysis based on pacbio .bax.h5 data. I already mapped the .h5 data to the reference genome and got .cmp.h5/.sam results.

    In order to get IPD information, I knew from the pacbio website that kinetics tools can be used for extracting IPD from .cmp.h5. But I couldn't find detailed documentations of how to install/use the kinetics tools.

    Has anyone ever used such tools to get IPD information and corresponding analysis of methylation? Or are there any other methods for these analysis?

    Thanks a lot

  • #2
    By far the easiest way is to use Pacbio's complete software suite, https://github.com/PacificBiosciences/SMRT-Analysis, http://www.pacb.com/support/software-downloads/particularly if you are working with bacterial modifications?

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    • #3
      Thank you!

      I am working on bacterial modifications.
      I know that SMRT tools can be used to analysis epigenetics and I find the protocol here.
      GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.


      But the examples used in the protocol are based on visualized SMRT tools, I am trying to run those data on linux platform so command lines are required. I have already aligned the h5 to reference genome using pbalign, but the following steps are not the clear to me.

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      • #4
        It is not straightforward to run the analysis outside of a SMRT Analysis pipeline. SMRT Analysis can be installed on linux, and the analysis carried out via the command line
        Code:
        smrtpipe.py --examples
        or web interface. If you are having problems installing SMRT Analysis, it can be used via an Amazon ami https://github.com/PacificBioscience...MRT-Portal-AMI, or virtual machine https://github.com/PacificBioscience...achine-Install

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        • #5
          When I tried to test with smrtpipe.py --example, I found that the python module "SMRTpipe" was missing. After I installed SMRT analysis tools, I found a lot of similar modules missing and I had to install them when I noticed that one was missing. Why is this happening? Do I misinstall it at the very beginning?

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          • #6
            Originally posted by qihualiang View Post
            When I tried to test with smrtpipe.py --example, I found that the python module "SMRTpipe" was missing. After I installed SMRT analysis tools, I found a lot of similar modules missing and I had to install them when I noticed that one was missing. Why is this happening? Do I misinstall it at the very beginning?


            Did you follow the install guide?

            http://www.pacb.com/wp-content/uploa...ion-v2-3-0.pdf

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            • #7
              Originally posted by gconcepcion View Post
              Yes, I followed it. But I guess it's the problem that I don't have root access and I solved these by installing some packages with my local python.

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