Parameters used in PASA for annotation polishing. run_spliced_aligners.pl:-N=5 #script validate_alignments_in_db.dbi validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=90 validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=80 validate_alignments_in_db.dbi:--MAX_INTRON_LENGTH=10000 validate_alignments_in_db.dbi:--NUM_BP_PERFECT_SPLICE_BOUNDARY=0 #Overlap stringiency assign_clusters_by_stringent_alignment_overlap.dbi:-L=30 #script subcluster_builder.dbi subcluster_builder.dbi:-m=50 #annotation comparison cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP=50 cDNA_annotation_comparer.dbi:--MIN_PERCENT_PROT_CODING=30 cDNA_annotation_comparer.dbi:--MIN_PERID_PROT_COMPARE=50 cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_FL_COMPARE=70 cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_NONFL_COMPARE=70 cDNA_annotation_comparer.dbi:--MIN_PERCENT_ALIGN_LENGTH=70 cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP_GENE_REPLACE=90 cDNA_annotation_comparer.dbi:--MAX_UTR_EXONS=5