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EI-CoreBioinformatics / portcullis

Splice junction analysis and filtering from BAM files
https://ei-corebioinformatics.github.io/portcullis/
GNU General Public License v3.0
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Use score instead of coverage for the BED/GFF/GTF output #19

Closed lucventurini closed 8 years ago

lucventurini commented 8 years ago

Having the score instead of the coverage would help in Mikado by allowing to have a clear idea of how good each of the junctions is. We could implement it as a choice in Portcullis, ie default behaviour provide the score, otherwise provide the coverage.

A separate problem is how to deal with pre-filtering junctions file. There the coverage might be used by default.

An additional possibility would be to put this information in the file header.

lucventurini commented 8 years ago

Addendum: this could also be used during the filtering stage. So it would be possible to do the filtering once, and use any combination of tools to filter the desired TAB/BED/GTF/GFF3 files in output.

maplesond commented 8 years ago

This should be addressed in the latest release. coverage is used during the junction analysis stage, but filtering score is added for the filtering stage.