Difference between revisions of "PASA"
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The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites. | The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites. | ||
| − | + | <!--Modules--> | |
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| − | <!-- --> | ||
==Required Modules== | ==Required Modules== | ||
[[Modules|modules documentation]] | [[Modules|modules documentation]] | ||
===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
* HPC_PASA_BIN - executable directory. | * HPC_PASA_BIN - executable directory. | ||
* HPC_PASA_CONF - config file directory. | * HPC_PASA_CONF - config file directory. | ||
| − | {{#if: {{#var: exe}}|== | + | <!--Additional--> |
| + | {{#if: {{#var: exe}}|==Additional Information== | ||
===Tools and variables=== | ===Tools and variables=== | ||
* <code>UNIVECDB</code> environment variable is set to the location of the UniVec database for use by seqclean. | * <code>UNIVECDB</code> environment variable is set to the location of the UniVec database for use by seqclean. | ||
Revision as of 19:25, 10 August 2012
Description
The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
Required Modules
Serial
- pasa
System Variables
- HPC_{{#uppercase:pasa}}_DIR - installation directory
- HPC_PASA_BIN - executable directory.
- HPC_PASA_CONF - config file directory.
Additional Information
Tools and variables
UNIVECDBenvironment variable is set to the location of the UniVec database for use by seqclean.
Databases
- The MySQL server used by PASA has been configured to allow the pasaadmin user to create databases with names that end in _pasa only. So, to run pasa your configuration file such as alignAssembly.config or conf.txt must have MySQL configuration similar to the following entry:
MYSQLDB=test_run_pasa
The example configuration files are located in /apps/pasa/20110520/pasa_conf ($HPC_PASA_CONF) directory.
Web Portal
You can visualize the results of your PASA run by going to the "http://pasa.hpc.ufl.edu/cgi-bin/status_report.cgi?db=$MYSQL_DB" URL where "$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.