Difference between revisions of "PASA"
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Brian Haas also behind this Splice Alignment tool. | Brian Haas also behind this Splice Alignment tool. | ||
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| + | = Using PASA = | ||
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| + | PASA has quite alot of parts and it could almost be seen as a mini-pipeline. THe canonical command for running it on the marvin cluster is: | ||
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| + | Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2 | ||
| + | <ins>Explanation</ins>: | ||
| + | * '''-c''' is a configuration file which you, the user, needs to set up. The database name you choose for the analysis needs to be specified in this. | ||
| + | * '''-C''' is for creating a new database, if there is one there already, the command will fail. | ||
| + | * '''--CPU''' is for the number of threads. | ||
= Installation = | = Installation = | ||
Revision as of 16:47, 24 November 2017
Contents
Introduction
Brian Haas also behind this Splice Alignment tool.
Using PASA
PASA has quite alot of parts and it could almost be seen as a mini-pipeline. THe canonical command for running it on the marvin cluster is:
Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2
Explanation:
- -c is a configuration file which you, the user, needs to set up. The database name you choose for the analysis needs to be specified in this.
- -C is for creating a new database, if there is one there already, the command will fail.
- --CPU is for the number of threads.
Installation
- The PASA mysql user requires full privileges so it can create databases, which it apparently does for every analysis.
- these privileges must also exist for '%', so that all the nodes can also do this.
- the issue of a key being too long for mysql was corrected by replacing 1000 with 500 in this line.
gene_id varchar(1000) default NULL,
in the $PASAHOME/schema/cdna_alignment_mysqlschema file on line 174, which was also an issue back in 2013 (see links section).
Links
- Yours truly posing a question in May 2013! here.
