docs(Execution workflow): update output file specifications for reporting region-level 'polyA site usage scores' #380

Related to #372 & it's PR #373

We have tools like LABRAT, APAlyzer that report their own metrics to represent relative PAS usage within a gene/terminal exon, rather than the relative usage of each individual polyA site within the region. We want to be able consider tools like this for relative quantification benchmarking event.

Tasks:

• Update execution_workflows/execution_output_specification.md - specify an execution workflow output file format to capture the region-level 'score' for relative PAS usage.
• Add example output files corresponding to the new specification in execution_workflows/example_output_files.

We are currently prioritising the implementation of fractional PAS usage quantification benchmark. For now this issue serves as a reminder to come back to this if we can with references to previous work/discussions!

Previous suggestion in PR #373

This generated some discussion and was probably not the consensus view. See comments from @dominikburri and my response.

Format 05

This BED file contains positions of regions (e.g. terminal exons of genes, whole genes) and the relative usage values for each identified region in the score column.

Fields:

• chrom - the name of the chromosome
• chromStart - the starting position of the feature in the chromosome; this corresponds to the first nucleotide of the region (e.g. terminal exon, gene); the starting position is 0-based, i.e. the first base on the chromosome is numbered 0
• chromEnd - the ending position of the feature in the chromosome; this corresponds to the last nucleotide of the region.
• name - defines the name of the identified region. It's recommended to use a conventional identifier (e.g. Ensembl transcript ID, gene ID)
• score - relative usage value for the identified region
• strand - defines the strand; either "." (=no strand) or "+" or "-".