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Baltica output

Baltica framework produces two files as output:
- an R markdown report - an excel spreadsheet

Note

If available, the orthogonal dataset is treated as a new method named orthogonal.

Baltica table spreadsheet

  • results/baltica_table_{proj_name}.xlsx

The spreadsheet contains the complete set of coordinate output by methods and comparisons. In addition, there are a column for the combination of methods and comparisons plus the columns for the annotation:

  • coordinates: junction genomic coordinate in the format: {chr}:{start}-{end}:{strand} (strand omitted if none)
  • score columns: in the format: {method}_{comparisons}
  • is_novel: whether the splicing junction is or not annotated
  • gene_name: the gene name obtained from the de novo annotation workflow
  • transcript_name: transcript name from the de novo annotation
  • class_code: transcript class association to the reference annotation transcript, please see Fig 1 in the GFF Utilities paper for details
  • exon_number: pairs of exon numbers from the de novo annotation. First of the pair is the donor exon if the feature is the positive strand; otherwise acceptor
  • as_type: type of AS for each junction exon skipping (ES), alternative 3' splice site (A3SS), alternative 5' splice site (A5SS)

Currently, the HTML report comprises two sections:

Common splice junctions

The upset plot shows the combination of distinct sets of calls (score > 0.95) from each method and contrast. The plot helps to compare the common calls among sets. The complement sets are ignored, as these sets usually have a high number.

Baltica table

This interactive HTML table provides the top 1,000 (or baltica_max_table in the configuration file) sorted by the sum of the scores. Extra annotation is available upon clicking on ▶. In addition, the coordinates columns link to the UCSC genome browser. Regional URL for UCSC GB can be selected with ucsc_url, and assembly should be selected with the assembly configuration

Baltica report configuration

Change the following options on your project configuration to change the report:

  • project_authors: name of the persons running the project
  • project_title: name of the files and report title
  • baltica_max_table: maximum number of rows on the HTML table
  • assembly: assembly used for linking with the genome browser
  • ucsc_url: URL for the genome browser, like http://genome-euro.ucsc.edu for the European mirror

Reproducibility

This section provides the information necessary to reproduce the report, including project configuration and R package version.