I'm new to PacBio data analysis. This question is quite simply/silly. Basically I'm asking how to run secondary analysis by command lines without using SMRT pipe.
The purpose is to detect DNA methylation. PacBio provides a package "SMRTanalysis" to deal with the primary and secondary analysis.
In the secondary analysis, based on its "SMRT pipe reference guide" from this page (http://pacbiodevnet.com/), the protocol is "RS_modificaiton_detection" which includes four modules:
• P_Filter
• P_Mapping
• P_GenomicConsensus
• P_Modification Detection
In each model, I think the program calls multiple individual scripts to accomplish the task. But I can't find any manual online that tells what exactly those scripts are. (If you use SMRTpipe, you don't have to know what scripts each module calls, but I'm trying to run it without Pipe)
The facility here has installed an instance of SMRTanalysis with all its scripts, but only its Portal and View, no Pipe. I'm wondering if anyone knows what scripts are used in each module so that users can run the scripts by themselves instead of using Pipe.
What I found was this page (https://github.com/PacificBioscience...tible-Software) that lists the Compatible Softwares.
I think I can figure out some of them to do the same work as the SMRT "Modification_detection" workflow. Please let me know if the following is correct:
1. Mapping: BLASR
2. GenomicConcensus: Quiver
3. Modification detection: kineticsTools
But I'm missing "filtering". Could anyone tell me which program does "filter"?
Thanks.
The purpose is to detect DNA methylation. PacBio provides a package "SMRTanalysis" to deal with the primary and secondary analysis.
In the secondary analysis, based on its "SMRT pipe reference guide" from this page (http://pacbiodevnet.com/), the protocol is "RS_modificaiton_detection" which includes four modules:
• P_Filter
• P_Mapping
• P_GenomicConsensus
• P_Modification Detection
In each model, I think the program calls multiple individual scripts to accomplish the task. But I can't find any manual online that tells what exactly those scripts are. (If you use SMRTpipe, you don't have to know what scripts each module calls, but I'm trying to run it without Pipe)
The facility here has installed an instance of SMRTanalysis with all its scripts, but only its Portal and View, no Pipe. I'm wondering if anyone knows what scripts are used in each module so that users can run the scripts by themselves instead of using Pipe.
What I found was this page (https://github.com/PacificBioscience...tible-Software) that lists the Compatible Softwares.
I think I can figure out some of them to do the same work as the SMRT "Modification_detection" workflow. Please let me know if the following is correct:
1. Mapping: BLASR
2. GenomicConcensus: Quiver
3. Modification detection: kineticsTools
But I'm missing "filtering". Could anyone tell me which program does "filter"?
Thanks.
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