PASA

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Introduction

Brian Haas also behind this Splice Alignment tool.

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.