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lecture_notes:04-16-2010 [2010/04/17 00:22] svasili |
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- | ====== Newbler assembly of POG ====== | + | ====== Newbler assembly on POG ====== |
====== Overview ====== | ====== Overview ====== | ||
Outlines how Kevin assembled 454 data of Pyrobaculum oguniense (POG) using Newbler 2.3 version. | Outlines how Kevin assembled 454 data of Pyrobaculum oguniense (POG) using Newbler 2.3 version. | ||
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* make.log - keeps track of what happened. | * make.log - keeps track of what happened. | ||
- | ====== Things to remember while running assembly tools====== | + | ====== Things to remember while running assembly tools ====== |
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- | * All the assemblies should be listed under /campusdata/BME235/assemblies. | + | * All the assemblies should be listed under /campusdata/BME235/assemblies. |
- | * Include .cshrc file in your path. | + | * Include .cshrc file in your path. |
- | * Its better to run the tool in the current working directory. | + | * Its better to run the tool in the current working directory. |
- | * Create a README file in each new directory and it should contain all the necessary stuff required to run the assembly tool. | + | * Create a README file in each new directory and it should contain all the necessary stuff required to run the assembly tool. |
- | * Create Makefile for each assembly tool. (Makefile for newbler_assembly tool is in /campusdata/BME235/assemblies/Pog//newbler-assembly1/). You can use it as a template and modify the data source and the expected coverage as required. Makefile should be considered as "a book for lab protocols". | + | * Create Makefile for each assembly tool. (Makefile for newbler_assembly tool is in /campusdata/BME235/assemblies/Pog//newbler-assembly1/). You can use it as a template and modify the data source and the expected coverage as required. Makefile should be considered as "a book for lab protocols". |
- | * Its always better to say append to make.log in Makefile. | + | * Its always better to say append to make.log in Makefile. |
- | * Wiki page for assembly tools should contain a summary of how to run the tool and other things that might be useful to look at. | + | * Wiki page for assembly tools should contain a summary of how to run the tool and other things that might be useful to look at. |