PASA not adding UTRs to existing annotations

[Anjali]

Hi everyone,

PASA showed a finished run without any error. But it shows examining 0 contigs and not adding UTRs to my existing annotations.

Following  are the steps i am doing:

create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -d pasa_db.sqlite -S cdna_alignment_sqliteschema

Load_Current_Gene_Annotations.dbi -c alignAssembly.config -g hybrid_1.fasta -P brakernew.gff3

Launch_PASA_pipeline.pl -c annotationCompare.config -A -g hybrid_1.fasta -t stringtie_transcripts.fasta --ALT_SPLICE --TRANSDECODER

[Brian Haas]

Hi,

I think you didn't run the alignment assembly step

https://github.com/PASApipeline/PASApipeline/wiki/PASA_alignment_assembly#transcript-alignments-followed-by-alignment-assembly

That's needed before doing the annotation comparison/update.

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas