lecture_notes:04-16-2010
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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 |
lecture_notes:04-16-2010 [2010/04/20 03:04] karplus added python2.6.5 |
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| * 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 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. | ||
lecture_notes/04-16-2010.txt ยท Last modified: 2010/04/20 03:09 by karplus
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