Parameters
input_file: 20101125_LUjt8_2_hg19_ensembl59_G_iCLIP_TDP-43_SH-SY5Y_bedGraph-cDNA-hits-in-genome.bed.gz
input_res_type: single hits in whole-genome, cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 5

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 13213
[x-link sites] used in any map: 1923 (14.55%)
[single hits in whole-genome, cDNA counts] total: 13213
[single hits in whole-genome, cDNA counts] used in any map: 2165 (15.71%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map
exon-intron	-300; 300	561	4.25%	29.17%	576	4.18%	26.61%
intron-exon	-300; 300	460	3.48%	23.92%	471	3.42%	21.76%
5-ncRNA	-1000; 300	228	1.73%	11.86%	295	2.14%	13.63%
ncRNA-3	-300; 1000	232	1.76%	12.06%	365	2.65%	16.86%
ORF-3UTR	-300; 300	63	0.48%	3.28%	65	0.47%	3.00%
5UTR-ORF	-300; 300	12	0.09%	0.62%	12	0.09%	0.55%
inter-5UTR	-1000; 300	47	0.36%	2.44%	47	0.34%	2.17%
3UTR-inter	-300; 1000	115	0.87%	5.98%	117	0.85%	5.40%
inter-5	-1000; 300	183	1.38%	9.52%	246	1.78%	11.36%
3-inter	-300; 1000	284	2.15%	14.77%	417	3.03%	19.26%
BP best in intron	-300; 100	434	3.28%	22.57%	453	3.29%	20.92%

Download statistics in tab-delimited format.
Download graphs in tab-delimited format.

RNAmap exon-intron

junction is at position zero.
upstream is regions of type: ORF, 3UTR, 5UTR
downstream is regions of type: intron

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	526	3.98%	27.35%	93.76%	475	1.03137
anti	35	0.26%	1.82%	6.24%	35	0.0686275
both	561	4.25%	29.17%	100.00%	510	1.1
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	540	3.92%	24.94%	93.75%	475	1.05882
anti	36	0.26%	1.66%	6.25%	35	0.0705882
both	576	4.18%	26.61%	100.00%	510	1.12941

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr20:329036@+	-47; 300	NRSN2	5; 0	5; 0
chr17:4192523@-	-90; 300	UBE2G1	4; 0	4; 0
chr14:62211531@+	-55; 300	HIF1A	4; 0	4; 0
chr10:79616486@-	-82; 300	DLG5	4; 0	4; 0
chr1:11140554@-	-207; 300	EXOSC10	4; 0	5; 0
chr1:1158622@-	-57; 300	SDF4	4; 0	4; 0
chr3:93699326@+	-135; 300	ARL13B	3; 0	3; 0
chr3:15003999@+	-43; 300	NR2C2	3; 0	3; 0
chr2:214167306@+	-35; 300	SPAG16	3; 0	3; 0
chr12:76462687@-	-43; 300	NAP1L1	3; 0	3; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr20:329036@+	-47; 300	NRSN2	5; 0	5; 0
chr1:11140554@-	-207; 300	EXOSC10	4; 0	5; 0
chr17:4192523@-	-90; 300	UBE2G1	4; 0	4; 0
chr14:62211531@+	-55; 300	HIF1A	4; 0	4; 0
chr10:103590823@-	-50; 300	KCNIP2	3; 0	4; 0
chr10:79616486@-	-82; 300	DLG5	4; 0	4; 0
chr1:1158622@-	-57; 300	SDF4	4; 0	4; 0
chr3:93699326@+	-135; 300	ARL13B	3; 0	3; 0
chr3:15003999@+	-43; 300	NR2C2	3; 0	3; 0
chr2:214167306@+	-35; 300	SPAG16	3; 0	3; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap intron-exon

junction is at position zero.
upstream is regions of type: intron
downstream is regions of type: ORF, 3UTR, 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	427	3.23%	22.20%	92.83%	395	1
anti	33	0.25%	1.72%	7.17%	32	0.0772834
both	460	3.48%	23.92%	100.00%	427	1.07728
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	438	3.18%	20.23%	92.99%	395	1.02576
anti	33	0.24%	1.52%	7.01%	32	0.0772834
both	471	3.42%	21.76%	100.00%	427	1.10304

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr10:43604478@+	-300; 100	RET	5; 0	6; 0
chr1:156834145@+	-300; 37	NTRK1	4; 0	4; 0
chr5:179041959@-	-293; 300	HNRNPH1	3; 0	3; 0
chr5:14479369@+	-300; 45	TRIO	3; 0	3; 0
chr12:50594666@-	-300; 54	LIMA1	3; 0	3; 0
chr1:161182879@+	-218; 46	NDUFS2	3; 0	3; 0
chrX:118754013@-	-300; 300	SEPT6	2; 0	3; 0
chr8:53536418@-	-300; 40	RB1CC1	2; 0	2; 0
chr8:11640711@+	-300; 98	NEIL2	2; 0	2; 0
chr7:100203127@+	-145; 154	PCOLCE	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr10:43604478@+	-300; 100	RET	5; 0	6; 0
chr1:156834145@+	-300; 37	NTRK1	4; 0	4; 0
chrX:118754013@-	-300; 300	SEPT6	2; 0	3; 0
chr5:179041959@-	-293; 300	HNRNPH1	3; 0	3; 0
chr5:14479369@+	-300; 45	TRIO	3; 0	3; 0
chr19:48201890@+	-300; 74	GLTSCR1	2; 0	3; 0
chr12:50594666@-	-300; 54	LIMA1	3; 0	3; 0
chr1:161182879@+	-218; 46	NDUFS2	3; 0	3; 0
chrX:118820611@-	-300; 45	SEPT6	1; 0	2; 0
chr8:53536418@-	-300; 40	RB1CC1	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5-ncRNA

junction is at position zero.
upstream is regions of type: intron, inter, telo
downstream is regions of type: ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	131	0.99%	6.81%	57.46%	56	0.916084
anti	97	0.73%	5.04%	42.54%	87	0.678322
both	228	1.73%	11.86%	100.00%	143	1.59441
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	197	1.43%	9.10%	66.78%	56	1.37762
anti	98	0.71%	4.53%	33.22%	87	0.685315
both	295	2.14%	13.63%	100.00%	143	2.06294

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	42; 0	105; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	19; 0	22; 0
chr11:65269806@+	-1000; 29	MALAT1	8; 0	8; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chr7:601594@+	-1000; 26	AC147651.5	0; 3	0; 3
chr3:175394588@-	-1000; 300	RP11-744O11.2	0; 3	0; 3
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	3; 0	3; 0
chr4:66959859@+	-1000; 182	RP11-25H12.1, RP11-396M11.1	2; 0	2; 0
chr17:29582820@+	-1000; 34	AC004222.1, AC134669.1	2; 0	2; 0
chr17:29463276@+	-1000; 300	AC079915.1, AC134669.1	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	42; 0	105; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	19; 0	22; 0
chr11:65269806@+	-1000; 29	MALAT1	8; 0	8; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chr7:601594@+	-1000; 26	AC147651.5	0; 3	0; 3
chr3:175394588@-	-1000; 300	RP11-744O11.2	0; 3	0; 3
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	3; 0	3; 0
chr4:66959859@+	-1000; 182	RP11-25H12.1, RP11-396M11.1	2; 0	2; 0
chr19:56616784@+	-1000; 47	Y_RNA-ENSG00000223060	0; 1	0; 2
chr17:29582820@+	-1000; 34	AC004222.1, AC134669.1	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ncRNA-3

junction is at position zero.
upstream is regions of type: ncRNA
downstream is regions of type: intron, inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	161	1.22%	8.37%	69.40%	58	1.33058
anti	71	0.54%	3.69%	30.60%	63	0.586777
both	232	1.76%	12.06%	100.00%	121	1.91736
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	293	2.13%	13.53%	80.27%	58	2.42149
anti	72	0.52%	3.33%	19.73%	63	0.595041
both	365	2.65%	16.86%	100.00%	121	3.01653

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	229; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr7:110749322@-	-45; 1000	IMMP2L, snoU13-ENSG00000238922	2; 0	2; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 2	0; 2
chr7:605256@+	-260; 1000	AC147651.5	0; 2	0; 2
chr5:86595502@-	-56; 1000	U6-ENSG00000207452	0; 2	0; 2
chr4:71655925@-	-300; 1000	AC009570.3	0; 2	0; 2
chr22:19409368@+	-78; 1000	AC000079.1	0; 2	0; 2
chr19:35491390@+	-73; 1000	AC020907.6, GRAMD1A-ENSG00000248852	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	229; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chrX:77218386@+	-169; 1000	ATP7A, RP5-1000K24.2	1; 0	2; 0
chr7:110749322@-	-45; 1000	IMMP2L, snoU13-ENSG00000238922	2; 0	2; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 2	0; 2
chr7:605256@+	-260; 1000	AC147651.5	0; 2	0; 2
chr5:86595502@-	-56; 1000	U6-ENSG00000207452	0; 2	0; 2
chr4:71655925@-	-300; 1000	AC009570.3	0; 2	0; 2
chr22:19409368@+	-78; 1000	AC000079.1	0; 2	0; 2

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ORF-3UTR

junction is at position zero.
upstream is regions of type: ORF
downstream is regions of type: 3UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	58	0.44%	3.02%	92.06%	54	0.983051
anti	5	0.04%	0.26%	7.94%	5	0.0847458
both	63	0.48%	3.28%	100.00%	59	1.0678
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	60	0.44%	2.77%	92.31%	54	1.01695
anti	5	0.04%	0.23%	7.69%	5	0.0847458
both	65	0.47%	3.00%	100.00%	59	1.10169

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:62496037@-	-203; 149	DDX5	2; 0	2; 0
chr16:29831075@+	-100; 300	C16orf53	2; 0	2; 0
chr15:93567935@+	-167; 300	CHD2	2; 0	2; 0
chr1:65897747@+	-131; 300	LEPROT	2; 0	2; 0
chr9:124094881@+	-85; 120	GSN	1; 0	1; 0
chr7:127222064@-	-300; 300	GCC1	1; 0	1; 0
chr7:92244026@-	-287; 300	CDK6	1; 0	1; 0
chr7:44101313@+	-300; 300	DBNL	1; 0	1; 0
chr6:121769142@+	-300; 300	GJA1	1; 0	1; 0
chr5:179263657@+	-111; 280	SQSTM1	1; 0	1; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr21:40547382@-	-104; 300	PSMG1	1; 0	2; 0
chr17:62496037@-	-203; 149	DDX5	2; 0	2; 0
chr17:33338983@-	-92; 300	RFFL	1; 0	2; 0
chr16:29831075@+	-100; 300	C16orf53	2; 0	2; 0
chr15:93567935@+	-167; 300	CHD2	2; 0	2; 0
chr1:65897747@+	-131; 300	LEPROT	2; 0	2; 0
chr9:124094881@+	-85; 120	GSN	1; 0	1; 0
chr7:127222064@-	-300; 300	GCC1	1; 0	1; 0
chr7:92244026@-	-287; 300	CDK6	1; 0	1; 0
chr7:44101313@+	-300; 300	DBNL	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5UTR-ORF

junction is at position zero.
upstream is regions of type: 5UTR
downstream is regions of type: ORF

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	11	0.08%	0.57%	91.67%	11	0.916667
anti	1	0.01%	0.05%	8.33%	1	0.0833333
both	12	0.09%	0.62%	100.00%	12	1
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	11	0.08%	0.51%	91.67%	11	0.916667
anti	1	0.01%	0.05%	8.33%	1	0.0833333
both	12	0.09%	0.55%	100.00%	12	1

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr4:183838009@-	-198; 67	DCTD	1; 0	1; 0
chr4:71588290@+	-290; 89	RUFY3	1; 0	1; 0
chr4:39064134@+	-142; 260	KLHL5	1; 0	1; 0
chr22:41677047@-	-297; 56	RANGAP1	1; 0	1; 0
chr16:89980628@+	-52; 300	AC092143.1	1; 0	1; 0
chr15:83735902@-	-102; 200	BTBD1	1; 0	1; 0
chr15:66995596@+	-300; 300	SMAD6	1; 0	1; 0
chr13:110438399@-	-258; 300	IRS2	0; 1	0; 1
chr13:45010763@-	-109; 62	TSC22D1	1; 0	1; 0
chr11:67007678@+	-52; 81	KDM2A	1; 0	1; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr4:183838009@-	-198; 67	DCTD	1; 0	1; 0
chr4:71588290@+	-290; 89	RUFY3	1; 0	1; 0
chr4:39064134@+	-142; 260	KLHL5	1; 0	1; 0
chr22:41677047@-	-297; 56	RANGAP1	1; 0	1; 0
chr16:89980628@+	-52; 300	AC092143.1	1; 0	1; 0
chr15:83735902@-	-102; 200	BTBD1	1; 0	1; 0
chr15:66995596@+	-300; 300	SMAD6	1; 0	1; 0
chr13:110438399@-	-258; 300	IRS2	0; 1	0; 1
chr13:45010763@-	-109; 62	TSC22D1	1; 0	1; 0
chr11:67007678@+	-52; 81	KDM2A	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5UTR

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	23	0.17%	1.20%	48.94%	22	0.522727
anti	24	0.18%	1.25%	51.06%	22	0.545455
both	47	0.36%	2.44%	100.00%	44	1.06818
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	23	0.17%	1.06%	48.94%	22	0.522727
anti	24	0.17%	1.11%	51.06%	22	0.545455
both	47	0.34%	2.17%	100.00%	44	1.06818

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr5:140027369@-	-1000; 101	NDUFA2	0; 2	0; 2
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr13:26828275@+	-1000; 251	CDK8	2; 0	2; 0
chrX:112084042@-	-1000; 66	AMOT	1; 0	1; 0
chr9:103115220@-	-1000; 84	TEX10	1; 0	1; 0
chr9:3526003@-	-1000; 129	RFX3	1; 0	1; 0
chr8:103876396@-	-1000; 181	AZIN1	1; 0	1; 0
chr8:28747697@-	-1000; 149	INTS9	0; 1	0; 1
chr8:24814623@-	-1000; 297	NEFL	1; 0	1; 0
chr8:144778323@+	-385; 300	AC105219.1	1; 0	1; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr5:140027369@-	-1000; 101	NDUFA2	0; 2	0; 2
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr13:26828275@+	-1000; 251	CDK8	2; 0	2; 0
chrX:112084042@-	-1000; 66	AMOT	1; 0	1; 0
chr9:103115220@-	-1000; 84	TEX10	1; 0	1; 0
chr9:3526003@-	-1000; 129	RFX3	1; 0	1; 0
chr8:103876396@-	-1000; 181	AZIN1	1; 0	1; 0
chr8:28747697@-	-1000; 149	INTS9	0; 1	0; 1
chr8:24814623@-	-1000; 297	NEFL	1; 0	1; 0
chr8:144778323@+	-385; 300	AC105219.1	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3UTR-inter

junction is at position zero.
upstream is regions of type: 3UTR
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	96	0.73%	4.99%	83.48%	83	0.950495
anti	19	0.14%	0.99%	16.52%	18	0.188119
both	115	0.87%	5.98%	100.00%	101	1.13861
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	98	0.71%	4.53%	83.76%	83	0.970297
anti	19	0.14%	0.88%	16.24%	18	0.188119
both	117	0.85%	5.40%	100.00%	101	1.15842

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chrX:48779303@-	-300; 1000	OTUD5	2; 0	2; 0
chr8:439941@-	-300; 1000	C8orf42	2; 0	2; 0
chr7:30199534@+	-192; 1000	C7orf41	2; 0	2; 0
chr3:167726463@-	-300; 1000	GOLIM4	2; 0	2; 0
chr19:55741146@-	-300; 257	SAPS1	2; 0	2; 0
chr16:8985949@-	-300; 1000	USP7	2; 0	2; 0
chr12:65642107@+	-300; 1000	LEMD3	2; 0	2; 0
chr11:77926340@-	-300; 1000	GAB2	2; 0	2; 0
chr10:88495822@+	-300; 1000	LDB3	0; 2	0; 2

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chr13:31710760@-	-231; 1000	HSPH1	1; 0	3; 0
chrX:48779303@-	-300; 1000	OTUD5	2; 0	2; 0
chr8:439941@-	-300; 1000	C8orf42	2; 0	2; 0
chr7:30199534@+	-192; 1000	C7orf41	2; 0	2; 0
chr3:167726463@-	-300; 1000	GOLIM4	2; 0	2; 0
chr19:55741146@-	-300; 257	SAPS1	2; 0	2; 0
chr16:8985949@-	-300; 1000	USP7	2; 0	2; 0
chr12:65642107@+	-300; 1000	LEMD3	2; 0	2; 0
chr11:77926340@-	-300; 1000	GAB2	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	86	0.65%	4.47%	46.99%	40	0.68254
anti	97	0.73%	5.04%	53.01%	86	0.769841
both	183	1.38%	9.52%	100.00%	126	1.45238
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	149	1.08%	6.88%	60.57%	40	1.18254
anti	97	0.70%	4.48%	39.43%	86	0.769841
both	246	1.78%	11.36%	100.00%	126	1.95238

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	42; 0	105; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chr3:175394588@-	-1000; 300	RP11-744O11.2	0; 3	0; 3
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	3; 0	3; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 2	0; 2
chr5:140027369@-	-1000; 101	NDUFA2	0; 2	0; 2
chr21:38739235@+	-1000; 300	DYRK1A	2; 0	2; 0
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr13:26828275@+	-1000; 251	CDK8	2; 0	2; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	2; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	42; 0	105; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chr3:175394588@-	-1000; 300	RP11-744O11.2	0; 3	0; 3
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	3; 0	3; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 2	0; 2
chr5:140027369@-	-1000; 101	NDUFA2	0; 2	0; 2
chr21:38739235@+	-1000; 300	DYRK1A	2; 0	2; 0
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr13:26828275@+	-1000; 251	CDK8	2; 0	2; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3-inter

junction is at position zero.
upstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	220	1.67%	11.44%	77.46%	106	1.34969
anti	64	0.48%	3.33%	22.54%	57	0.392638
both	284	2.15%	14.77%	100.00%	163	1.74233
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	353	2.56%	16.30%	84.65%	106	2.16564
anti	64	0.46%	2.96%	15.35%	57	0.392638
both	417	3.03%	19.26%	100.00%	163	2.55828

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	229; 0
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chrX:48779303@-	-300; 1000	OTUD5	2; 0	2; 0
chr8:439941@-	-300; 1000	C8orf42	2; 0	2; 0
chr7:30199534@+	-192; 1000	C7orf41	2; 0	2; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 2	0; 2
chr7:605256@+	-260; 1000	AC147651.5	0; 2	0; 2
chr4:71655925@-	-300; 1000	AC009570.3	0; 2	0; 2

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	229; 0
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr13:31710760@-	-231; 1000	HSPH1	1; 0	3; 0
chrX:48779303@-	-300; 1000	OTUD5	2; 0	2; 0
chr8:439941@-	-300; 1000	C8orf42	2; 0	2; 0
chr7:30199534@+	-192; 1000	C7orf41	2; 0	2; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 2	0; 2
chr7:605256@+	-260; 1000	AC147651.5	0; 2	0; 2

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap "BP best in intron"

BP is at position zero.
upstream is usptream of branch point
downstream is downstream of branch point

[eps]

x-links and BPs distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [BPs] in map	[x-link sites] per unique [BP]
same	412	3.12%	21.42%	94.93%	375	1.0404
anti	22	0.17%	1.14%	5.07%	21	0.0555556
both	434	3.28%	22.57%	100.00%	396	1.09596
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [BPs] in map	[single hits in whole-genome, cDNA counts] per unique [BP]
same	430	3.12%	19.86%	94.92%	375	1.08586
anti	23	0.17%	1.06%	5.08%	21	0.0580808
both	453	3.29%	20.92%	100.00%	396	1.14394

Top 10 BPs with largest x-link sites sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	9; 0	13; 0
chr7:75660266@-	-300; 100	STYXL1	4; 0	4; 0
chr1:156834120@+	-300; 23	NTRK1	4; 0	4; 0
chr5:14479206@+	-300; 100	TRIO	3; 0	3; 0
chr11:94527725@+	-300; 100	AMOTL1	3; 0	3; 0
chrX:118754079@-	-300; 66	SEPT6	2; 0	3; 0
chr8:53536534@-	-300; 100	RB1CC1	2; 0	2; 0
chr6:105220056@-	-300; 100	HACE1	2; 0	2; 0
chr5:154214515@-	-300; 22	C5orf4	2; 0	2; 0
chr3:128205938@-	-300; 20	GATA2	2; 0	2; 0

Top 10 BPs with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	9; 0	13; 0
chr7:75660266@-	-300; 100	STYXL1	4; 0	4; 0
chr1:156834120@+	-300; 23	NTRK1	4; 0	4; 0
chrX:118754079@-	-300; 66	SEPT6	2; 0	3; 0
chr5:14479206@+	-300; 100	TRIO	3; 0	3; 0
chr19:48201835@+	-300; 53	GLTSCR1	2; 0	3; 0
chr11:94527725@+	-300; 100	AMOTL1	3; 0	3; 0
chr9:36210576@+	-300; 43	CLTA	1; 0	2; 0
chr8:53536534@-	-300; 100	RB1CC1	2; 0	2; 0
chr6:105220056@-	-300; 100	HACE1	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.