Output

In the /output/directory/ (specific by -d), the following files are generated:

summary.tsv

cassette.tsv

tandem_cassette.tsv

alt5prime.tsv

alt3prime.tsv

alt3and5prime.tsv

alternate_first_exon.tsv

alternate_last_exon.tsv

p_alt5prime.tsv

p_alt3prime.tsv

mutually_exclusive.tsv

alternative_intron.tsv

exitron.tsv

other.tsv

constitutive.tsv (optional: see –keep-constitutive and –show-all-modules)

p_multi_gene_region.tsv (optional: see –multi-gene-regions)

For most users, we think the most important file is the summary file. Each row in the file corresponds to a Module, and the columns are as follows:

  1. Module: <Gene ID>_<N>

  2. Gene ID

  3. Gene Name

  4. Chr

  5. Strand

  6. LSV ID(s): <semi-colon separated LSV IDs>

  7. Cassette: <Count>

  8. Tandem Cassette: <Count>

  9. Alt 3: <Count>

  10. Alt 5: <Count>

  11. P_Alt 3: <Count>

  12. P_Alt 5: <Count>

  13. Alt 3 and Alt 5: <Count>

  14. MXE: <Count>

  15. Alternative Intron: <Count>

  16. ALE: <Count>

  17. AFE: <Count>

  18. P_ALE: <Count>

  19. P_AFE: <Count>

  20. Orphan Junction: <Count>

  21. Constitutive Junction: <Count> (Optional: see

    –keep-constitutive)

  22. Constitutive Intron: <Count> (Optional: see

    –keep-constitutive)

  23. Multi Exon Spanning: <Count>

  24. Exitron: <Count>

  25. Complex: <TRUE or FALSE>

Complex=False only if modules are comprised of a single event, OR meet specific

criteria such as: (1) only comprised of 1 Intron Retention and 1 P_Alt 5/3, or (2) only

comprised of 1 Tandem Cassette, 1 Multi Exon Spanning, and any number of

Constitutive Junctions

  1. Number of Events <Sum of Counts>

Sum of the event <Counts> across this module.

  1. Collapsed Event Name

Summarizes the types and counts of events in this module.

Tip: You can use Excel Pivot Table (Fields: ‘Module ID’ and ‘Collapsed Event Name’,

Rows: Collapsed Event Name, Values: Count of Module ID) to tabulate of all the

different types of modules in the summary.tsv file.