################### folder names and associated input files #############
SAMPLE_1\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind2-paired.fastq
SAMPLE_1\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind2-paired.fastq
SAMPLE_1\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind2-paired.fastq
SAMPLE_1\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind2-paired.fastq
SAMPLE_2\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind2-paired.fastq
SAMPLE_2\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind2-paired.fastq
SAMPLE_2\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind2-paired.fastq
SAMPLE_2\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind2-paired.fastq
#########################################################################

############################# MATS Report #############################
======================================================================
EventType	NumEvents.JC.only	SigEvents.JC.only	NumEvents.JC+readsOnTarget	SigEvents.JC+readsOnTarget
======================================================================
SE	33738	133 (71:62)	34244	145 (80:65)
MXE	4998	70 (28:42)	5064	114 (50:64)
A5SS	12445	144 (66:78)	12467	161 (72:89)
A3SS	18980	209 (95:114)	18999	214 (100:114)
RI	3786	122 (66:56)	3806	134 (66:68)
======================================================================
################# 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)
################################################