################### folder names and associated input files #############
SAMPLE_1\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort2-paired.fastq
SAMPLE_1\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort2-paired.fastq
SAMPLE_1\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort2-paired.fastq
SAMPLE_1\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort2-paired.fastq
SAMPLE_2\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort2-paired.fastq
SAMPLE_2\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort2-paired.fastq
SAMPLE_2\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort2-paired.fastq
SAMPLE_2\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort2-paired.fastq
#########################################################################

############################# MATS Report #############################
======================================================================
EventType	NumEvents.JC.only	SigEvents.JC.only	NumEvents.JC+readsOnTarget	SigEvents.JC+readsOnTarget
======================================================================
SE	39156	294 (199:95)	39739	350 (230:120)
MXE	6274	51 (28:23)	6358	65 (39:26)
A5SS	13928	99 (55:44)	13953	108 (61:47)
A3SS	21228	116 (64:52)	21238	117 (63:54)
RI	4129	31 (18:13)	4155	49 (25:24)
======================================================================
################# Report Legend ################
EventType: Type of AS event
	SE: Skipped exon
	MXE: Mutually exclusive exon
	A5SS: Alternative 5' splice site
	A3SS: Alternative 3' splice site
	RI: Retained intron
NumEvents.JC.only: total number of events detected using Junction Counts only
SigEvents.JC.only: number of significant events detected using Junction Counts only
	The numbers in the parentheses (n1:n2) indicate the number of significant events that have higher inclusion level for SAMPLE_1 (n1) or for SAMPLE_2 (n2)
NumEvents.JC+readsOnTarget: total number of events detected using both Junction Counts and reads on target
SigEvents.JC+readsOnTarget: number of significant events detected using both Junction Counts and reads on target
	The numbers in the parentheses (n1:n2) indicate the number of significant events that have higher inclusion level for SAMPLE_1 (n1) or for SAMPLE_2 (n2)
################################################