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lecture_notes:04-16-2010 [2010/04/19 18:41] jlong Mapping code, .rdb code for Makefile, 454NewblerMetrics |
lecture_notes:04-16-2010 [2010/04/19 19:40] karplus added a caveat about example that wasn't from the lecture, fixed indenting on last list |
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* Where -e 25 is specific to the Vibrio sequence coverage, and -noace prevents the building of an ace file (large file) which is used with CONSED. | * Where -e 25 is specific to the Vibrio sequence coverage, and -noace prevents the building of an ace file (large file) which is used with CONSED. | ||
* Slug is AT-rich, so Illumina data may be better than 454. | * Slug is AT-rich, so Illumina data may be better than 454. | ||
- | * rdb files were described as useful simple to create relational databases. An example of rdb file generation with a makefile is given below as implemented by Kevin's in /pluck/rachel/combined_cleaning1/Makefile . | + | * rdb files were described as useful simple to create relational databases. An example of rdb file generation with a makefile is given below as implemented by Kevin's in /pluck/rachel/combined_cleaning1/Makefile . Note that this example was **not** given in class, and is intended for pulling out a subset of the contigs, not making an rdb file for all contigs. |
<code> | <code> | ||
%.stats: %.ids | %.stats: %.ids | ||
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====== Things to remember while running assembly tools ====== | ====== Things to remember while running assembly tools ====== | ||
- | | + | |
- | * 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. |