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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: -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


  • -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.


  • 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).


  • Yours truly posing a question in May 2013! here.