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Old 02-04-2016, 10:21 AM   #1
qihualiang
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Default 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
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Old 02-04-2016, 02:56 PM   #2
rhall
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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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Old 02-05-2016, 12:32 AM   #3
qihualiang
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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.
https://github.com/PacificBioscience...Technical-Note

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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Old 02-05-2016, 10:10 AM   #4
rhall
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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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Old 02-09-2016, 09:51 AM   #5
qihualiang
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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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Old 02-10-2016, 12:40 PM   #6
gconcepcion
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Quote:
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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Old 02-11-2016, 10:39 AM   #7
qihualiang
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Quote:
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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