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PASA- Structural annotation of genome assembly

I ran both Trinity de novo and Trinity genome-guided assemblies and used PASA to update/compare my reference annotation in order to identify novel transcripts. After running the annotation comparison/update step, PASA produced the files postPASA.updates.gff3 and a corresponding BED file. I have two questions:
1. What exactly is included in postPASA.updates.gff3?
Does this file contain only PASA-identified novel transcripts and isoforms, or does it also include the original, unmodified reference transcripts/genes?

2. How can I extract the full nucleotide sequences of only the novel transcripts?
I would like to obtain FASTA sequences for all novel transcripts or isoforms introduced/modified by PASA. What is the recommended workflow or PASA utility for this?

Any suggestion would be appreciated.

pasa
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updated by colindaven colindaven • written by rachana • rachana

1 answer

1) from the documentation:

postPASA.updates.gff3 contains your original gene models PLUS any structural updates that PASA has made

so it seems that it does include both sets of genes.

2) To get the nucleotide sequence of the genes of interest: If i remember well there might be some utility included in the PASA package to extract nucleotide-seqs for certain genes. If not: you can also start from the BED file , extract the IDs for the genes of interest, use bedtools getfasta to extract the sequences (or extract the nucleo-seq for all genes and filter afterwards)

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written by lieven.sterck lieven.sterck

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