lecture_notes:04-16-2010
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lecture_notes:04-16-2010 [2010/04/17 00:22] svasili |
lecture_notes:04-16-2010 [2010/04/20 03:09] (current) karplus fixed punctuation that was messing up final list |
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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. | ||
| Line 12: | Line 13: | ||
| * Currently, tools are installed under /campusdata/BME235/bin/old_Newbler/. | * Currently, tools are installed under /campusdata/BME235/bin/old_Newbler/. | ||
| * Tools with prefix "gs" are not supposed to be run directly. | * Tools with prefix "gs" are not supposed to be run directly. | ||
| - | * Kevin has written several scripts in Python (version 2.6) which aid in building and analyzing genomes. Currently these scripts do not work as on Campusrocks, as the version of Python installed is 2.4 and it is under the process of being updated to version 2.6. | + | * Kevin has written several scripts in Python (version 2.6) which aid in building and analyzing genomes. Currently, these scripts do not work on Campusrocks, as the version of Python installed is 2.4 and it is under the process of being updated to version 2.6. (Python2.6.5 has now been installed in /campusdata/BME235/bin/ --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/19 20:03//) |
| * Newbler assembly tools take .sff (color space and quality data) files as input and converts them into .fna (fasta file with nucleotide information) files. | * Newbler assembly tools take .sff (color space and quality data) files as input and converts them into .fna (fasta file with nucleotide information) files. | ||
| * Good only with 454 data, and is not good on reads with length < 50. | * Good only with 454 data, and is not good on reads with length < 50. | ||
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| * Output : Generated in a separate directory called "assembly". Main outputs - .fna files and .qual files. Look at "/campusdata/BME235/assemblies/Pog/newbler-assembly1/assembly". | * Output : Generated in a separate directory called "assembly". Main outputs - .fna files and .qual files. Look at "/campusdata/BME235/assemblies/Pog/newbler-assembly1/assembly". | ||
| * make.log - keeps track of what happened. | * make.log - keeps track of what happened. | ||
| + | * Mapping to an existing genome, an example from Kevin Karplus /pluck/Vc/map23_scaffold | ||
| + | <code> | ||
| + | newMapping . | ||
| + | addRun . /projects/lowelab/users/course/karplus/Vc/sequencing/sff/*.sff | ||
| + | setRef . Vc.scaffold | ||
| + | runProject -e 25 -rst 0 -noace . | ||
| + | </code> | ||
| + | * 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. | ||
| + | * 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> | ||
| + | %.stats: %.ids | ||
| + | echo "name length numreads" > $@ | ||
| + | echo "S N N" >> $@ | ||
| + | grep '^>' < contigs_all.fa \ | ||
| + | | grep -f $*.ids \ | ||
| + | | sed 's/=/ /g' \ | ||
| + | | sed 's/>//' \ | ||
| + | | awk '{printf "%s\t%d\t%d\n", $$1, $$3, $$5}' \ | ||
| + | >> $@ | ||
| + | </code> | ||
| + | * If anyone finds good user based documentation or tutorials versus feature based documentation, please share them with the group. | ||
| + | * Don't copy sfffiles use soft links to data files. | ||
| + | * Useful output cam be found in /assembly/454NewblerMetrics.txt . The inputs, reads, bases (to calculate coverage= bases/ genome size), readAlignmentResults, inferredReadError (0.8%= OK), estimatedGenomeSize, consesusResults (largeContigMetrics, allContigs, ...) | ||
| + | | ||
| + | ====== Things to remember while running assembly tools ====== | ||
| - | ====== Things to remember while running assembly tools====== | + | * All the assemblies should be listed under /campusdata/BME235/assemblies. |
| - | + | * Include .cshrc file in your path. | |
| - | * All the assemblies should be listed under /campusdata/BME235/assemblies. | + | * Its better to run the tool in the current working directory. |
| - | * Include .cshrc file in your path. | + | * Create a README file in each new directory and it should contain all the necessary stuff required to run the assembly tool. |
| - | * Its better to run the tool in the current working directory. | + | * 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 a README file in each new directory and it should contain all the necessary stuff required to run the assembly tool. | + | * It is always better to say append to make.log in Makefile. |
| - | * 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. | + | |
| * 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. | ||
lecture_notes/04-16-2010.1271463779.txt.gz · Last modified: 2010/04/17 00:22 by svasili
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