Question: Launch_PASA_pipeline.pl options --stringent_alignment_overlap and --gene_overlap

[Kris Alavattam]

Hi Brian,

Are the two Launch_PASA_pipeline.pl options --stringent_alignment_overlap and --gene_overlap mutually exclusive (i.e., they can't be called together)? I ran an experiment in which I called Launch_PASA_pipeline.pl with both --stringent_alignment_overlap 30.0 and --gene_overlap 50.0 (having specified -L and a corresponding gff3 file with --annots). The resulting outfiles are equivalent to having called Launch_PASA_pipeline.pl with --stringent_alignment_overlap 30.0 alone (I wrote --stringent_alignment_overlap before -L, --annots, and --gene_overlap); also, the stderr messages are nearly equivalent (barring different directory names), and there's no mention of the gff3 file in the stderr messages.

In going back to review the documentation here, it seems that the two options are exclusive, e.g., with the sentence, "Also, as an alternative, if you have existing gene structure annotations that are reasonably accurate..." Is this right?

Thanks,
Kris

[Brian Haas]

Hi Kris,

Yes, these options are mutually exclusive, and the stringent alignment
overlap takes priority among the selections. I'll make that clear in
the usage for the next release.

best,

~b

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