*_cassette_event_counts_w_p_val.txt:
(1) N/K  - If "N", the event includes a novel splice junction.  "K", if all
junctions are annotated
(2) I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(3) Gene Name
(4) chr
(5) upstream intron coordinate(s) - a cassette exon may have multiple upstream
introns, separated by commas
(6) start coordinate of cassette exon
(7) end coordinate of cassette exon
(8) downstream intron coordinate(s) - a cassette exon may have multiple
downstream introns, separated by commas.
(9) Exclusion counts in Untreated
(10) Inclusion counts in Untreated -  Before adding exon reads from single
reads (paired end counts are included here)
(11) Exclusion counts in RNAi sample
(12) Inclusion counts in RNAi sample - Before adding exon reads from single
reads (paired end counts are included here)
(13) coordinate of cassette exon (used to count the number of single reads that
are contained in this region)
(14) Final Exclusion counts in Untreated
(15) Final Inclusion counts in Untreated (exon counts from single reads are
added here)
(16) Final Exclusion counts in RNAi
(17) Final Inclusion counts in RNAi (exon counts from single reads are added
here)
(18) raw p-val
(19) corrected p-val

*_alternative_donor_counts_w_p_val.txt
*_alternative_acceptor_counts_w_p_val.txt
(1) N/K  - If "N", the event includes a novel splice junction.  "K", if all
junctions are annotated
(2) I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(3) Gene Name
(4) chr
(5) start coordinate of the intron in the inclusion isoform
(6) end coordinate of the intron in the inclusion isoform
(7) coordinates of all other introns involved in the event, if multiple
introns, they are separated by commas
(8) Exclusion counts in Untreated
(9) Inclusion counts in Untreated -  Before adding exon reads from single reads
(paired end counts are included here)
(10) Exclusion counts in RNAi sample
(11) Inclusion counts in RNAi sample - Before adding exon reads from single
reads (paired end counts are included here)
(12) coordinate of the alternative region (note that this is not an exon, it is
the portion of the exon that is alternative; used in another script to count
the number of single reads that are contained in this region)
(13) Final Exclusion counts in Untreated
(14) Final Inclusion counts in Untreated (exon counts from single reads are
added here)
(15) Final Exclusion counts in RNAi
(16) Final Inclusion counts in RNAi (exon counts from single reads are added
here)
(17) raw p-val
(18) corrected p-val

*_alternative_first_exon_counts_w_p_val.txt
*_alternative_last_exon_counts_w_p_val.txt
(1) N/K  - If "N", the event includes a novel splice junction.  "K", if all
junctions are annotated
(2) I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(3) Gene Name
(4) chr
(5) start coordinate of the intron of the proximal exon
(6) end coordinate of the intron of the proximal exon
(7) coordinates of all other introns involved in the event, associated with
other exons. If multiple introns, they are separated by commas
(8) Exclusion counts in Untreated
(9) Inclusion counts in Untreated -  Before adding exon reads from single reads
(paired end counts are included here)
(10) Exclusion counts in RNAi sample
(11) Inclusion counts in RNAi sample - Before adding exon reads from single
reads (paired end counts are included here)
(12) coordinate of the proximal exon (used in another script to count the
number of single reads that are contained in this region)
(13) coordinate of the distal exon (used in another script to count the number
of single reads that are contained in this region)
(14) Final Exclusion counts in Untreated
(15) Final Inclusion counts in Untreated (exon counts from single reads are
added here)
(16) Final Exclusion counts in RNAi
(17) Final Inclusion counts in RNAi (exon counts from single reads are added
here)
(18) raw p-val
(19) corrected p-val

*_intron_retention_left_counts_w_p_val.txt
*_intron_retention_right_counts_w_p_val.txt
(You can refer to the figure that explains how the intron retention events are
calculated)
NOTE: This is not a stranded analysis, so left and right is with respect to the
genome.
(1)  I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(2) Gene Name
(3) chr
(4) position of splice site
(5) intron coordinate
(6) Exclusion counts in Untreated
(7) Inclusion counts in Untreated
(8) Exclusion counts in RNAi
(9) Inclusion counts in RNAi
(10) raw p-val
(11) corrected p-val

*_IR_events.txt
(Refer to Supplementary Figure 8 that explains how the intron retention events
are calculated)
Columns 1-20: Concatenation of the calculations of the left and right side of
the junction
(21) The intron coordinate
(22) raw combined-pval (the raw p-val from the left and right are used for this
calculation)
(23) corrected combined p-val

*_mutually_exclusive_counts_w_p_val.txt
(1) N/K  - If "N", the event includes a novel splice junction.  "K", if all
junctions are annotated
(2) I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(3) Gene Name
(4) chr
(5) Shared start coordinate of introns upstream of mutually exclusive exons
(6) Shared end coordinate of introns downstream of mutually exclusive exons
(7) Coordinate of the exon that is treated as the inclusion exon.  NOTE: The
exon that is chosen as the "inclusion" isoform is an arbitrary decision.
(8) Coordinates of all exons involved in the mutually exclusive event
(9) Exclusion counts in Untreated  -  Before adding exon reads from single
reads (paired end counts are included here)
(10) Inclusion counts in Untreated -  Before adding exon reads from single
reads (paired end counts are included here)
(11) Exclusion counts in RNAi sample  - Before adding exon reads from single
reads (paired end counts are included here)
(12) Inclusion counts in RNAi sample - Before adding exon reads from single
reads (paired end counts are included here)
(13) coordinate of inclusion exon (used to count the number of single reads
that
are contained in this region)
(14) coordinate(s) of all other exons (used to count the number of single reads
that
are contained in this region)
(15) Final Exclusion counts in Untreated (exon counts from single reads are
added here)
(16) Final Inclusion counts in Untreated (exon counts from single reads are
added here)
(17) Final Exclusion counts in RNAi (exon counts from single reads are
added here)
(18) Final Inclusion counts in RNAi (exon counts from single reads are added
here)
(19) raw p-val
(20) corrected p-val

*_multi_cassette_counts_w_p_val.txt (AKA coordinate cassette exons)
(1) N/K  - If "N", the event includes a novel splice junction.  "K", if all
junctions are annotated
(2) I/E - There was a shift toward the Inclusion isoform or Exclusion isoform
upon RNAi of the protein
(3) Gene Name
(4) chr
(5) Exclusion junction start
(6) Exclusion junction end
(7) Coordinates of all exons involved in event
(8) Exclusion counts in Untreated 
(9) Inclusion counts in Untreated -  Before adding exon reads from single
reads (paired end counts are included here)
(10) Exclusion counts in RNAi sample
(11) Inclusion counts in RNAi sample - Before adding exon reads from single
reads (paired end counts are included here)
(12) Coordinates of all exons involved in event (used to count the number of
single reads that
are contained in this region)
(13) Final Exclusion counts in Untreated 
(14) Final Inclusion counts in Untreated (exon counts from single reads are
added here)
(15) Final Exclusion counts in RNAi 
(16) Final Inclusion counts in RNAi (exon counts from single reads are added
here)
(17) raw p-val
(18) corrected p-val
