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archive:bioinformatic_tools:phrap [2010/04/08 21:58] svasili created |
archive:bioinformatic_tools:phrap [2010/04/21 23:55] svasili |
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* "Quality value Q = -10 log10( Pe ); where Q and Pe are respectively the quality value and error probability of a particular base call." | * "Quality value Q = -10 log10( Pe ); where Q and Pe are respectively the quality value and error probability of a particular base call." | ||
- | PHRAP documentation available [[http://www.phrap.org/phredphrap/phrap.html | here]] | + | PHRAP documentation available [[http://www.phrap.org/phredphrap/phrap.html | here]]. |
+ | |||
+ | Requires Consed or phrapview editors. | ||
+ | |||
+ | ===== Installation instructions ===== | ||
+ | Phrap is now installed under /campusdata/BME235/programs/phrap following instructions received from Phil Green. | ||
+ | |||
+ | Steps followed for installation : | ||
+ | <code> | ||
+ | zcat distrib.tar.Z | tar xvf - | ||
+ | make | ||
+ | </code> | ||
+ | |||
+ | ===== Other important instructions from Phil Green ===== | ||
+ | |||
+ | <code> | ||
+ | If you have datasets with more than 64,000 reads, or that include | ||
+ | sequences longer than 64,000 bp, you will need the .manyreads and/or | ||
+ | .longreads versions of phrap and cross_match. These are created using the | ||
+ | command | ||
+ | |||
+ | > make manyreads | ||
+ | |||
+ | If you are operating a non-commercial (academic or government) | ||
+ | computer facility which provides access to several independent | ||
+ | investigators, you are required by the licensing agreement to set the | ||
+ | permissions on the executables and source code to allow execute but | ||
+ | not read access, so that the programs may not be copied. | ||
+ | |||
+ | The documentation is in three .doc files: general.doc, phrap.doc, | ||
+ | and swat.doc. Please read it! | ||
+ | |||
+ | </code> | ||
+ | |||
+ | **NOTE** - Currently, the permissions set are : user and group has rwx and r-x permissions respectively, for the executable files and source code files. |