Adding UTR on existing annotation file.

[Priti Prasad]

Dear Brian,

I am using PASA for adding UTR locus to the existing genome annotation file by using this command -"/Launch_PASA_pipeline.pl -c pasa_conf/pasa.alignAssembly.Template.txt -C -r -R -g /data/PASA/model_genome.fasta --ALIGNERS blat,gmap -t /data/PASA/Trinity_new.fasta --transcribed_is_aligned_orient --annot_compare -L --annots /data/PASA/model_gene_model.gff3 --gene_overlap 50.0 --ALT_SPLICE --CPU 50". It gives number of outputs, in which final file is in gff3 format  "database.pasa_assemblies.gff3"  where UTR entries were not given.

Could you please suggest to me -

1. How I will update the UTR - (Whether I need to run pasa_asmbls_to_training_set.dbi separately on assemblies.fasta and  assemblies.gff3).

2. How I will report novel isoform or transcript (if any). 

Thank You

Priti