Parameters
input_file: 20090724_LUjt2_1_hg19_ensembl59_S_iCLIP_TDP-43_Brain-F24_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 90246
[x-link sites] used in any map: 16866 (18.69%)
[single hits (=G+T), cDNA counts] total: 90246
[single hits (=G+T), cDNA counts] used in any map: 24324 (21.47%)

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 (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	3982	4.41%	23.61%	4224	3.73%	17.37%
intron-exon	-300; 300	4360	4.83%	25.85%	4531	4.00%	18.63%
5-ncRNA	-1000; 300	2639	2.92%	15.65%	6485	5.72%	26.66%
ncRNA-3	-300; 1000	2046	2.27%	12.13%	4699	4.15%	19.32%
ORF-3UTR	-300; 300	993	1.10%	5.89%	1025	0.90%	4.21%
5UTR-ORF	-300; 300	236	0.26%	1.40%	251	0.22%	1.03%
inter-5UTR	-1000; 300	407	0.45%	2.41%	760	0.67%	3.12%
3UTR-inter	-300; 1000	1122	1.24%	6.65%	1158	1.02%	4.76%
inter-5	-1000; 300	2170	2.40%	12.87%	6102	5.39%	25.09%
3-inter	-300; 1000	2401	2.66%	14.24%	4418	3.90%	18.16%
BP best in intron	-300; 100	2270	2.52%	13.46%	2390	2.11%	9.83%

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	3732	4.14%	22.13%	93.72%	3439	1.01523
anti	250	0.28%	1.48%	6.28%	240	0.0680087
both	3982	4.41%	23.61%	100.00%	3676	1.08324
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3967	3.50%	16.31%	93.92%	3439	1.07916
anti	257	0.23%	1.06%	6.08%	240	0.0699129
both	4224	3.73%	17.37%	100.00%	3676	1.14908

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 (=G+T), cDNA counts] (same; anti)
chr7:139025365@+	-85; 256	C7orf55	18; 0	132; 0
chr19:17740047@-	-42; 300	UNC13A	9; 0	9; 0
chr2:133015100@-	-221; 224	NCRNA00164	8; 0	10; 0
chr5:883069@-	-226; 300	BRD9	7; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	7; 0	7; 0
chr19:46815910@+	-247; 300	HIF3A	7; 0	8; 0
chr16:57662765@+	-174; 300	GPR56	7; 0	8; 0
chr10:103590823@-	-50; 300	KCNIP2	7; 0	7; 0
chr9:114306712@+	-300; 300	ZNF483	5; 0	5; 0
chr7:1479559@-	-300; 300	MICALL2	5; 0	5; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:139025365@+	-85; 256	C7orf55	18; 0	132; 0
chr2:133015100@-	-221; 224	NCRNA00164	8; 0	10; 0
chr19:17740047@-	-42; 300	UNC13A	9; 0	9; 0
chr19:46815910@+	-247; 300	HIF3A	7; 0	8; 0
chr16:57662765@+	-174; 300	GPR56	7; 0	8; 0
chr5:883069@-	-226; 300	BRD9	7; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	7; 0	7; 0
chr10:103590823@-	-50; 300	KCNIP2	7; 0	7; 0
chr2:127827569@-	-48; 300	BIN1	4; 0	6; 0
chr11:497969@-	-86; 300	RNH1	5; 0	6; 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	4111	4.56%	24.37%	94.29%	3825	1.01406
anti	249	0.28%	1.48%	5.71%	236	0.0614208
both	4360	4.83%	25.85%	100.00%	4054	1.07548
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	4259	3.76%	17.51%	94.00%	3825	1.05057
anti	272	0.24%	1.12%	6.00%	236	0.0670942
both	4531	4.00%	18.63%	100.00%	4054	1.11766

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 (=G+T), cDNA counts] (same; anti)
chr22:39715115@-	-130; 42	RPL3	9; 0	16; 0
chr12:113565982@-	-300; 57	RASAL1	9; 0	9; 0
chr20:10286776@+	-300; 300	SNAP25	8; 0	8; 0
chr2:127811587@-	-300; 54	BIN1	6; 0	6; 0
chr2:47387942@-	-300; 300	CALM2	6; 0	8; 0
chr2:27274290@+	-196; 66	AGBL5	6; 0	35; 0
chr4:863744@-	-300; 300	GAK	5; 0	5; 0
chr2:175665014@-	-300; 300	CHN1	5; 0	5; 0
chr19:46834412@+	-300; 93	HIF3A	5; 0	8; 0
chr4:158284586@+	-135; 300	GRIA2	4; 0	4; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr2:27274290@+	-196; 66	AGBL5	6; 0	35; 0
chr22:39715115@-	-130; 42	RPL3	9; 0	16; 0
chr8:26221236@+	-300; 85	PPP2R2A	1; 1	10; 5
chr1:182356426@-	-300; 259	GLUL	1; 1	1; 11
chr12:113565982@-	-300; 57	RASAL1	9; 0	9; 0
chr20:10286776@+	-300; 300	SNAP25	8; 0	8; 0
chr2:47387942@-	-300; 300	CALM2	6; 0	8; 0
chr19:46834412@+	-300; 93	HIF3A	5; 0	8; 0
chr2:127811587@-	-300; 54	BIN1	6; 0	6; 0
chr4:863744@-	-300; 300	GAK	5; 0	5; 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	2022	2.24%	11.99%	76.62%	646	1.79255
anti	617	0.68%	3.66%	23.38%	493	0.546986
both	2639	2.92%	15.65%	100.00%	1128	2.33954
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	5691	5.02%	23.40%	87.76%	646	5.04521
anti	794	0.70%	3.26%	12.24%	493	0.703901
both	6485	5.72%	26.66%	100.00%	1128	5.74911

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 (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:109077@+	-758; 300	18S	206; 0	1012; 0
chrUn_gl000220:113347@+	-585; 300	28S	202; 0	1355; 0
chr11:65269806@+	-1000; 29	MALAT1	142; 0	196; 0
chr1:109642814@+	-1000; 210	snoU2-25	109; 0	462; 0
chrM:16022@-	-274; 34	J01415.14	25; 2	168; 2
chr14:20811565@-	-1000; 166	RNaseP_nuc-ENSG00000252678	23; 0	38; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	21; 0	74; 0
chr2:230045665@-	-1000; 89	AC006368.1, PID1	20; 0	50; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	20; 0	24; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	18; 0	25; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:113347@+	-585; 300	28S	202; 0	1355; 0
chrUn_gl000220:109077@+	-758; 300	18S	206; 0	1012; 0
chr1:109642814@+	-1000; 210	snoU2-25	109; 0	462; 0
chr11:65269806@+	-1000; 29	MALAT1	142; 0	196; 0
chrM:16022@-	-274; 34	J01415.14	25; 2	168; 2
chr2:27273131@-	-1000; 42	AC013472.6	0; 16	0; 144
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	21; 0	74; 0
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	9; 0	68; 0
chr1:148241464@+	-1000; 82	U1-ENSG00000207501	13; 0	68; 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	1470	1.63%	8.72%	71.85%	516	1.59783
anti	576	0.64%	3.42%	28.15%	409	0.626087
both	2046	2.27%	12.13%	100.00%	920	2.22391
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3881	3.43%	15.96%	82.59%	516	4.21848
anti	818	0.72%	3.36%	17.41%	409	0.88913
both	4699	4.15%	19.32%	100.00%	920	5.10761

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 (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:110946@+	-300; 539	18S	202; 0	1514; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chrM:15953@+	-33; 309	J01415.6	6; 25	50; 160
chr11:62609089@-	-96; 978	U2-ENSG00000222328	30; 0	61; 0
chrM:4327@-	-36; 1000	J01415.13	0; 23	0; 57
chrM:15954@-	-34; 606	J01415.14	6; 15	25; 66
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:110946@+	-300; 539	18S	202; 0	1514; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chrM:15953@+	-33; 309	J01415.6	6; 25	50; 160
chrM:15954@-	-34; 606	J01415.14	6; 15	25; 66
chr14:74055527@-	-37; 1000	AC005225.1	3; 0	74; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	30; 0	61; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	11; 0	58; 0
chrM:4327@-	-36; 1000	J01415.13	0; 23	0; 57

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	938	1.04%	5.56%	94.46%	761	1.17104
anti	55	0.06%	0.33%	5.54%	43	0.0686642
both	993	1.10%	5.89%	100.00%	801	1.2397
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	967	0.85%	3.98%	94.34%	761	1.20724
anti	58	0.05%	0.24%	5.66%	43	0.0724095
both	1025	0.90%	4.21%	100.00%	801	1.27965

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 (=G+T), cDNA counts] (same; anti)
chr10:22825820@-	-195; 300	PIP5K2A	15; 0	18; 0
chrX:139865739@-	-300; 158	CDR1	0; 11	0; 11
chr10:73822514@-	-74; 300	SPOCK2	10; 0	11; 0
chrX:103045717@+	-132; 300	PLP1	6; 0	6; 0
chr2:55199719@-	-300; 198	RTN4	5; 0	5; 0
chr2:199011686@+	-92; 300	PLCL1	5; 0	5; 0
chr17:8063722@-	-233; 300	VAMP2	5; 0	5; 0
chr16:67472427@-	-82; 253	ATP6V0D1	5; 0	8; 0
chr16:89981552@+	-300; 300	AC092143.1	5; 0	5; 0
chrX:148564273@-	-173; 300	IDS	4; 0	4; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr10:22825820@-	-195; 300	PIP5K2A	15; 0	18; 0
chrX:139865739@-	-300; 158	CDR1	0; 11	0; 11
chr10:73822514@-	-74; 300	SPOCK2	10; 0	11; 0
chr16:67472427@-	-82; 253	ATP6V0D1	5; 0	8; 0
chrX:103045717@+	-132; 300	PLP1	6; 0	6; 0
chr2:55199719@-	-300; 198	RTN4	5; 0	5; 0
chr2:199011686@+	-92; 300	PLCL1	5; 0	5; 0
chr17:8063722@-	-233; 300	VAMP2	5; 0	5; 0
chr16:89981552@+	-300; 300	AC092143.1	5; 0	5; 0
chrX:148564273@-	-173; 300	IDS	4; 0	4; 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	211	0.23%	1.25%	89.41%	170	1.12234
anti	25	0.03%	0.15%	10.59%	18	0.132979
both	236	0.26%	1.40%	100.00%	188	1.25532
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	223	0.20%	0.92%	88.84%	170	1.18617
anti	28	0.02%	0.12%	11.16%	18	0.148936
both	251	0.22%	1.03%	100.00%	188	1.33511

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 (=G+T), cDNA counts] (same; anti)
chr6:31508971@-	-66; 265	BAT1	11; 0	17; 0
chr2:61764828@-	-277; 66	XPO1	8; 0	8; 0
chrX:139866530@-	-96; 300	CDR1	0; 7	0; 7
chr4:71588290@+	-290; 89	RUFY3	5; 0	6; 0
chr16:89980628@+	-52; 300	AC092143.1	4; 0	4; 0
chr16:1756340@+	-74; 159	MAPK8IP3	3; 0	3; 0
chr13:45010763@-	-109; 62	TSC22D1	3; 0	3; 0
chrX:148586666@-	-105; 51	IDS	2; 0	2; 0
chr6:7542148@+	-171; 85	DSP	0; 2	0; 2
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr6:31508971@-	-66; 265	BAT1	11; 0	17; 0
chr2:61764828@-	-277; 66	XPO1	8; 0	8; 0
chrX:139866530@-	-96; 300	CDR1	0; 7	0; 7
chr4:71588290@+	-290; 89	RUFY3	5; 0	6; 0
chr16:89980628@+	-52; 300	AC092143.1	4; 0	4; 0
chr16:1756340@+	-74; 159	MAPK8IP3	3; 0	3; 0
chr15:31196866@+	-76; 300	MTMR15	2; 0	3; 0
chr13:45010763@-	-109; 62	TSC22D1	3; 0	3; 0
chrX:148586666@-	-105; 51	IDS	2; 0	2; 0
chr9:35748969@-	-128; 300	GBA2	1; 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-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	171	0.19%	1.01%	42.01%	154	0.555195
anti	236	0.26%	1.40%	57.99%	159	0.766234
both	407	0.45%	2.41%	100.00%	308	1.32143
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	179	0.16%	0.74%	23.55%	154	0.581169
anti	581	0.51%	2.39%	76.45%	159	1.88636
both	760	0.67%	3.12%	100.00%	308	2.46753

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 (=G+T), cDNA counts] (same; anti)
chr13:41635409@+	-1000; 200	WBP4	0; 19	0; 161
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51
chr15:80737492@-	-1000; 74	AC016705.1	0; 7	0; 8
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 8
chrX:139866722@-	-1000; 96	CDR1	0; 6	0; 7
chr20:47894962@-	-1000; 248	ZNFX1	0; 6	0; 6
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 5
chr1:151030233@+	-1000; 300	MLLT11	1; 4	1; 4
chr18:47340272@-	-1000; 209	ACAA2	0; 4	0; 4

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr13:41635409@+	-1000; 200	WBP4	0; 19	0; 161
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51
chr17:37026255@+	-1000; 93	LASP1	0; 2	0; 18
chr15:80737492@-	-1000; 74	AC016705.1	0; 7	0; 8
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 8
chrX:139866722@-	-1000; 96	CDR1	0; 6	0; 7
chr20:47894962@-	-1000; 248	ZNFX1	0; 6	0; 6
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 5
chr1:151030233@+	-1000; 300	MLLT11	1; 4	1; 4

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	914	1.01%	5.42%	81.46%	767	0.987041
anti	208	0.23%	1.23%	18.54%	166	0.224622
both	1122	1.24%	6.65%	100.00%	926	1.21166
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	938	0.83%	3.86%	81.00%	767	1.01296
anti	220	0.19%	0.90%	19.00%	166	0.237581
both	1158	1.02%	4.76%	100.00%	926	1.25054

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 (=G+T), cDNA counts] (same; anti)
chrX:139865423@-	-158; 1000	CDR1	0; 8	0; 9
chr17:8024297@-	-294; 1000	HES7	6; 0	10; 0
chr5:71502853@+	-300; 1000	MAP1B	5; 0	5; 0
chr3:115528639@-	-241; 1000	LSAMP	5; 0	5; 0
chr18:72102961@-	-300; 1000	FAM69C	5; 0	6; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 5	0; 8
chr9:111899165@-	-283; 1000	C9orf4	4; 0	4; 0
chr5:139496321@+	-300; 1000	PURA	4; 0	4; 0
chr3:9543479@-	-206; 1000	LHFPL4	4; 0	4; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 4	0; 4

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:8024297@-	-294; 1000	HES7	6; 0	10; 0
chrX:139865423@-	-158; 1000	CDR1	0; 8	0; 9
chr16:67471456@+	-275; 1000	HSD11B2	0; 5	0; 8
chr18:72102961@-	-300; 1000	FAM69C	5; 0	6; 0
chr5:71502853@+	-300; 1000	MAP1B	5; 0	5; 0
chr3:115528639@-	-241; 1000	LSAMP	5; 0	5; 0
chr9:111899165@-	-283; 1000	C9orf4	4; 0	4; 0
chr9:77302117@+	-300; 1000	RORB	3; 0	4; 0
chr7:102740021@-	-100; 1000	NAPEPLD	0; 2	0; 4
chr7:75956114@-	-300; 1000	YWHAG	3; 0	4; 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	1223	1.36%	7.25%	56.36%	437	1.23911
anti	947	1.05%	5.61%	43.64%	560	0.959473
both	2170	2.40%	12.87%	100.00%	987	2.19858
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	4045	3.57%	16.63%	66.29%	437	4.09828
anti	2057	1.82%	8.46%	33.71%	560	2.08409
both	6102	5.39%	25.09%	100.00%	987	6.18237

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 (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 224	0; 947
chrUn_gl000220:109077@+	-758; 300	18S	206; 0	1012; 0
chrUn_gl000220:113347@+	-585; 300	28S	202; 0	1355; 0
chr1:109642814@+	-1000; 210	snoU2-25	109; 0	462; 0
chr14:20811565@-	-1000; 166	RNaseP_nuc-ENSG00000252678	23; 0	38; 0
chr13:41635409@+	-1000; 200	WBP4	0; 19	0; 161
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr9:79186648@+	-1000; 151	AL161626.1	16; 0	44; 0
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr22:43011249@+	-1000; 75	U12-ENSG00000199382	14; 0	31; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:113347@+	-585; 300	28S	202; 0	1355; 0
chrUn_gl000220:109077@+	-758; 300	18S	206; 0	1012; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 224	0; 947
chr1:109642814@+	-1000; 210	snoU2-25	109; 0	462; 0
chr13:41635409@+	-1000; 200	WBP4	0; 19	0; 161
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	9; 0	68; 0
chr1:148241464@+	-1000; 82	U1-ENSG00000207501	13; 0	68; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51

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	1803	2.00%	10.69%	75.09%	979	1.27331
anti	598	0.66%	3.55%	24.91%	445	0.422316
both	2401	2.66%	14.24%	100.00%	1416	1.69562
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3784	3.34%	15.56%	85.65%	979	2.67232
anti	634	0.56%	2.61%	14.35%	445	0.44774
both	4418	3.90%	18.16%	100.00%	1416	3.12006

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 (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:110946@+	-300; 539	18S	202; 0	1514; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr14:50053596@+	-150; 1000	RN7SL1	17; 0	33; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 0
chrX:108297359@-	-216; 1000	RN28S1	0; 11	0; 15
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 11	0; 11

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:110946@+	-300; 539	18S	202; 0	1514; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr9:79186950@+	-151; 1000	AL161626.1	6; 0	35; 0
chr14:50053596@+	-150; 1000	RN7SL1	17; 0	33; 0
chr6:26574925@+	-300; 1000	AL121936.1	3; 0	16; 0

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	2074	2.30%	12.30%	91.37%	1805	1.03908
anti	196	0.22%	1.16%	8.63%	192	0.0981964
both	2270	2.52%	13.46%	100.00%	1996	1.13727
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	2186	1.93%	8.99%	91.46%	1805	1.09519
anti	204	0.18%	0.84%	8.54%	192	0.102204
both	2390	2.11%	9.83%	100.00%	1996	1.19739

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 (=G+T), cDNA counts] (same; anti)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	18; 0	23; 0
chr13:27829210@+	-300; 100	SNORD102	11; 0	19; 0
chr12:113566108@-	-300; 100	RASAL1	10; 0	10; 0
chr5:138614713@+	-297; 24	MATR3	9; 0	9; 0
chr20:2634908@+	-300; 100	SNORD110	9; 0	10; 0
chr19:2337060@+	-300; 100	AC004410.1	9; 0	9; 0
chr12:6619768@+	-224; 24	NCAPD2	8; 0	9; 0
chr9:130210892@-	-238; 100	SNORA65	7; 0	11; 0
chr11:8707006@+	-177; 100	SNORA3-ENSG00000212607	7; 0	7; 0
chr9:125642528@-	-109; 100	SNORD90	6; 0	10; 0

Top 10 BPs with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr10:88649475@+	-300; 100	U1-ENSG00000200176	5; 0	33; 0
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	18; 0	23; 0
chr13:27829210@+	-300; 100	SNORD102	11; 0	19; 0
chr9:130210892@-	-238; 100	SNORA65	7; 0	11; 0
chr9:125642528@-	-109; 100	SNORD90	6; 0	10; 0
chr20:2634908@+	-300; 100	SNORD110	9; 0	10; 0
chr12:113566108@-	-300; 100	RASAL1	10; 0	10; 0
chr5:138614713@+	-297; 24	MATR3	9; 0	9; 0
chr19:2337060@+	-300; 100	AC004410.1	9; 0	9; 0
chr12:6619768@+	-224; 24	NCAPD2	8; 0	9; 0

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