PASA is adding few UTRs

[Anjali]

Hi everyone

PASA alignment and assembly command worked fine with only one thread.

But post update, PASA is only giving 49 UTRs for 14245 genes. 

Can anyone please help? Why it is doing so?

Do I need to mention some parameters in the config file?

[Brian Haas]

After running the alignment assembly, be sure to rerun the annotation comparison step.

If you're able to get the pasaweb portal operating, that's a good way to get an overview of the kinds of updates that happened.

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Brian J. Haas
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[Anjali .]

Yes,

After the alignment assembly step, I loaded the annotations and then performed the annotation comparision step.

1. Launch_PASA_pipeline.pl -c align assembly.config -C -R -h hybrid_1.fasta -t transcripts_renamed.fasta.clean -T -u transcripts_renamed.fasta -f FL_accs.txt —ALIGNERS blat —CPU 1

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

3. Launch_PASA_pipeline.pl -c annotationComparep.config -A -g hybrid_1.fasta -t transcripts_renamed.fasta --ALT_SPLICE --TRANSDECODER

[Brian Haas]

ok, another thing to check is that your genome contig ids in the hybrid_1.fasta match up perfectly with those in the brakernew.gff3