Questions: Running Launch_PASA_pipeline.pl in "gene_overlap mode" with a gff3 that contains whole-chromosome annotations: Effect on how --gene_overlap operates?

[Kris Alavattam]

Hi Brian,

Happy New Year! When calling Launch_PASA_pipeline.pl in "gene_overlap mode", I used "Saccharomyces_cerevisiae.R64-1-1.108.gff3" as the corresponding annotation (i.e., the input to argument --annots).

However, we just realized that "Saccharomyces_cerevisiae.R64-1-1.108.gff3", an official Ensembl annotation for S. cerevisiae, includes annotations for whole chromosomes among its many features; these annotations for whole chromosomes appear as giant chromosome-wide blocks when viewing the gff3 in IGV and other genome browsers (please see attached screenshot). This concerned us because it raises the possibility that, when using gene_overlap mode, all transcripts would be clustered regardless of the percent value supplied to --gene_overlap because all transcripts overlap the chromosome annotation. Do you know if this is the case? If so, then it would appear that I need to edit the Ensembl gff3 to remove the whole-chromosome annotations—and perhaps other features. In that case, do you have any opinions on what features I should specifically retain in the gff3? I was thinking to cut everything out except mRNA annotations? Or maybe that doesn't really matter—especially in comparison to the whole-chromosome annotations.

Anyway, thank you,

Kris

[Brian Haas]

Hi Kris,

I'm pretty sure PASA will parse and use only the features that are annotated as genes.  The chromosome features are probably labeled as regions or some other non-gene type feature.  If you're concerned, you could just edit them out of the gff3 before importing it into pasa.

best,

~b

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