predict UTRs using PASA

Question

[ingobulla]

Hi,

I would like to update a gene prediction without UTRs using PASA in order to add UTRs to the gene prediction. I have tried to get the example provided on PASA Tutorial - Annotation Comparisons and Annotation Updates running but executing the code

SAMPLE_DIR=/home/ingo/opt/PASApipeline-pasa-v2.2.0/sample_data
Launch_PASA_pipeline.pl -c $SAMPLE_DIR/annotCompare.config -r -C   # I use this command to reset the MySQL DB
Load_Current_Gene_Annotations.dbi -c $SAMPLE_DIR/alignAssembly.config -g $SAMPLE_DIR/genome_sample.fasta -P $SAMPLE_DIR/orig_annotations_sample.gff3
Launch_PASA_pipeline.pl -c $SAMPLE_DIR/annotCompare.config -A -g $SAMPLE_DIR/genome_sample.fasta -t $SAMPLE_DIR/all_transcripts.fasta.clean
grep -c "utr" $SAMPLE_DIR/orig_annotations_sample.gff3   # result: 138
grep -c "utr" sample_mydb_pasa.gene_structures_post_PASA_updates.6068.gff3   # result: 138

I don't get any new UTRs nor any changes in the UTRs of the original prediction. In fact, the original prediction doesn't seem to change at all as far as I can tell.

Has anyone an idea what the problem might be here?

[lieven.sterck]

138 UTRs out of how many genes?

perhaps there simply is not more data support for UTRs ?