lecture_notes:04-16-2010
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| * Kevin ran the assembly tool on POG 454 data under /campusdata/BME235/assemblies/Pog. | * Kevin ran the assembly tool on POG 454 data under /campusdata/BME235/assemblies/Pog. | ||
| * The README file in the directory contains important information about the assembly. | * The README file in the directory contains important information about the assembly. | ||
| - | * Info about tools installed is listed in bioinformatic_tools [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. | + | * Info about tools installed is listed in bioinformatic_tools [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. Info about how to run the De novo as well as Mapping assembly tools is also included there. |
| * Currently tools are installed under /campusdata/BME235/bin/old_Newbler/. | * Currently tools are installed under /campusdata/BME235/bin/old_Newbler/. | ||
| + | * Its better to run the tool in the current working directory. | ||
| * Tools with prefix "gs" are not supposed to be run directly. | * Tools with prefix "gs" are not supposed to be run directly. | ||
| + | * 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, is not good on reads < 50bp. | ||
| + | * Example to run the De novo tool on data is shown below. The code is taken from [[https://banana-slug.soe.ucsc.edu/bioinformatic_tools:gs_de_novo_assembler | GS De Novo Assembler]]. | ||
| + | <code> | ||
| + | newAssembly . | ||
| + | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | ||
| + | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | ||
| + | runProject -e 50 . | ||
| + | </code> | ||
| + | * Where, -e 50 is an important parameter -> implies expected coverage and it defaults to 50. | ||
| + | |||
lecture_notes/04-16-2010.txt · Last modified: 2010/04/20 03:09 by karplus
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