Parameters
input_file: 20101125_LUjt8_3_hg19_ensembl59_S_iCLIP_TDP-43_SH-SY5Y_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: 22248
[x-link sites] used in any map: 6400 (28.77%)
[single hits (=G+T), cDNA counts] total: 22248
[single hits (=G+T), cDNA counts] used in any map: 7862 (30.29%)

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	1080	4.85%	16.88%	1129	4.35%	14.36%
intron-exon	-300; 300	1370	6.16%	21.41%	1503	5.79%	19.12%
5-ncRNA	-1000; 300	561	2.52%	8.77%	1064	4.10%	13.53%
ncRNA-3	-300; 1000	499	2.24%	7.80%	755	2.91%	9.60%
ORF-3UTR	-300; 300	1155	5.19%	18.05%	1425	5.49%	18.13%
5UTR-ORF	-300; 300	47	0.21%	0.73%	48	0.18%	0.61%
inter-5UTR	-1000; 300	114	0.51%	1.78%	117	0.45%	1.49%
3UTR-inter	-300; 1000	1377	6.19%	21.52%	1621	6.24%	20.62%
inter-5	-1000; 300	531	2.39%	8.30%	839	3.23%	10.67%
3-inter	-300; 1000	1846	8.30%	28.84%	2328	8.97%	29.61%
BP best in intron	-300; 100	472	2.12%	7.38%	495	1.91%	6.30%

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	1017	4.57%	15.89%	94.17%	891	1.07278
anti	63	0.28%	0.98%	5.83%	57	0.0664557
both	1080	4.85%	16.88%	100.00%	948	1.13924
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	1065	4.10%	13.55%	94.33%	891	1.12342
anti	64	0.25%	0.81%	5.67%	57	0.0675105
both	1129	4.35%	14.36%	100.00%	948	1.19093

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)
chr22:38687371@-	-285; 177	CSNK1E	10; 0	13; 0
chr7:135613418@-	-300; 300	MTPN	6; 0	7; 0
chrX:70685855@+	-300; 131	TAF1	5; 0	5; 0
chr9:114306712@+	-300; 300	ZNF483	5; 0	5; 0
chr10:54077417@+	-300; 133	DKK1	5; 0	6; 0
chrX:39910497@-	-300; 300	BCOR	4; 0	4; 0
chr8:99057169@-	-73; 300	RPL30	4; 0	4; 0
chr3:197400831@-	-267; 300	KIAA0226	4; 0	4; 0
chr21:34949840@-	-194; 300	DONSON	4; 0	4; 0
chr21:27425550@-	-134; 300	APP	4; 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)
chr10:105174908@+	-74; 300	PDCD11	2; 0	14; 0
chr22:38687371@-	-285; 177	CSNK1E	10; 0	13; 0
chr7:135613418@-	-300; 300	MTPN	6; 0	7; 0
chr10:54077417@+	-300; 133	DKK1	5; 0	6; 0
chrX:70685855@+	-300; 131	TAF1	5; 0	5; 0
chr9:114306712@+	-300; 300	ZNF483	5; 0	5; 0
chr21:27425550@-	-134; 300	APP	4; 0	5; 0
chrX:39910497@-	-300; 300	BCOR	4; 0	4; 0
chr8:99057169@-	-73; 300	RPL30	4; 0	4; 0
chr3:197400831@-	-267; 300	KIAA0226	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 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	1286	5.78%	20.09%	93.87%	1077	1.11535
anti	84	0.38%	1.31%	6.13%	76	0.0728534
both	1370	6.16%	21.41%	100.00%	1153	1.1882
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	1404	5.41%	17.86%	93.41%	1077	1.21769
anti	99	0.38%	1.26%	6.59%	76	0.085863
both	1503	5.79%	19.12%	100.00%	1153	1.30356

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)
chr3:64502796@-	-300; 300	ADAMTS9	52; 0	99; 0
chr4:174253388@-	-291; 267	HMGB2	16; 0	33; 0
chr2:242291357@+	-300; 300	SEPT2	7; 0	8; 0
chr10:33200597@-	-108; 111	ITGB1	7; 0	7; 0
chr10:73048324@+	-300; 82	UNC5B	7; 0	8; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	7; 0
chr20:57485737@+	-141; 255	GNAS	5; 0	5; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	5; 0
chr1:26227577@-	-160; 260	STMN1	5; 0	5; 0
chr9:139247508@+	-300; 49	GPSM1	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)
chr3:64502796@-	-300; 300	ADAMTS9	52; 0	99; 0
chr4:174253388@-	-291; 267	HMGB2	16; 0	33; 0
chr8:15480586@+	-300; 86	TUSC3	3; 0	10; 0
chr2:242291357@+	-300; 300	SEPT2	7; 0	8; 0
chr10:73048324@+	-300; 82	UNC5B	7; 0	8; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	7; 0
chr12:104709554@+	-300; 60	TXNRD1	2; 0	7; 0
chr11:61547313@+	-133; 44	C11orf9	0; 1	0; 7
chr10:33200597@-	-108; 111	ITGB1	7; 0	7; 0
chr20:57485737@+	-141; 255	GNAS	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	357	1.60%	5.58%	63.64%	118	1.51271
anti	204	0.92%	3.19%	36.36%	121	0.864407
both	561	2.52%	8.77%	100.00%	236	2.37712
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	813	3.13%	10.34%	76.41%	118	3.44492
anti	251	0.97%	3.19%	23.59%	121	1.06356
both	1064	4.10%	13.53%	100.00%	236	4.50847

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)
chr1:109642814@+	-1000; 210	snoU2-25	70; 0	267; 0
chrUn_gl000220:109077@+	-758; 300	18S	50; 0	85; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	50; 0	232; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:113347@+	-585; 300	28S	28; 0	31; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:16022@-	-274; 34	J01415.14	9; 0	18; 0
chrM:576@+	-288; 35	J01415.1	3; 5	4; 6
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 6	0; 6
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7

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)
chr1:109642814@+	-1000; 210	snoU2-25	70; 0	267; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	50; 0	232; 0
chrUn_gl000220:109077@+	-758; 300	18S	50; 0	85; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:113347@+	-585; 300	28S	28; 0	31; 0
chrM:16022@-	-274; 34	J01415.14	9; 0	18; 0
chr19:58024440@-	-1000; 33	hsa-mir-1274b	1; 0	13; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:576@+	-288; 35	J01415.1	3; 5	4; 6
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7

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	350	1.57%	5.47%	70.14%	127	1.45228
anti	149	0.67%	2.33%	29.86%	115	0.618257
both	499	2.24%	7.80%	100.00%	241	2.07054
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	576	2.22%	7.33%	76.29%	127	2.39004
anti	179	0.69%	2.28%	23.71%	115	0.742739
both	755	2.91%	9.60%	100.00%	241	3.13278

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)
chr11:65271080@+	-300; 1000	MALAT1	117; 0	291; 0
chrUn_gl000220:110946@+	-300; 539	18S	50; 0	72; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	18; 0	24; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chrM:15953@+	-33; 309	J01415.6	0; 9	0; 18
chr7:131812561@+	-122; 1000	AC093106.4	0; 8	0; 10
chr7:149018954@-	-114; 1000	AC004941.5	6; 0	9; 0
chr5:149408910@-	-52; 1000	snoU13-ENSG00000238369	0; 6	0; 6
chr8:99056338@+	-185; 1000	SNORA72-ENSG00000245970	0; 4	0; 4
chr2:120979498@-	-300; 1000	TMEM185B	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)
chr11:65271080@+	-300; 1000	MALAT1	117; 0	291; 0
chrUn_gl000220:110946@+	-300; 539	18S	50; 0	72; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	18; 0	24; 0
chrM:15953@+	-33; 309	J01415.6	0; 9	0; 18
chr21:37438950@+	-54; 1000	U6-ENSG00000200213	0; 1	0; 11
chr7:131812561@+	-122; 1000	AC093106.4	0; 8	0; 10
chr7:149018954@-	-114; 1000	AC004941.5	6; 0	9; 0
chr19:781001@-	-300; 1000	AC006273.2	2; 0	8; 0
chr5:149408910@-	-52; 1000	snoU13-ENSG00000238369	0; 6	0; 6

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	1132	5.09%	17.69%	98.01%	600	1.8527
anti	23	0.10%	0.36%	1.99%	12	0.0376432
both	1155	5.19%	18.05%	100.00%	611	1.89034
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	1392	5.36%	17.71%	97.68%	600	2.27823
anti	33	0.13%	0.42%	2.32%	12	0.0540098
both	1425	5.49%	18.13%	100.00%	611	2.33224

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)
chr7:92244026@-	-287; 300	CDK6	49; 0	68; 0
chr7:100806072@-	-56; 142	VGF	33; 0	182; 0
chr7:26252043@+	-171; 300	CBX3	23; 0	29; 0
chr16:67472427@-	-82; 253	ATP6V0D1	23; 0	28; 0
chrX:40465007@+	-98; 300	ATP6AP2	13; 0	14; 0
chr5:122359566@-	-66; 300	PPIC	13; 0	14; 0
chr4:174448424@-	-51; 300	HAND2	11; 0	16; 0
chr1:149876562@-	-93; 300	SV2A	11; 0	14; 0
chr1:36181229@-	-300; 300	C1orf216	10; 0	11; 0
chr4:148465132@+	-300; 300	EDNRA	9; 0	11; 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)
chr7:100806072@-	-56; 142	VGF	33; 0	182; 0
chr7:92244026@-	-287; 300	CDK6	49; 0	68; 0
chr7:26252043@+	-171; 300	CBX3	23; 0	29; 0
chr16:67472427@-	-82; 253	ATP6V0D1	23; 0	28; 0
chr4:174448424@-	-51; 300	HAND2	11; 0	16; 0
chrX:40465007@+	-98; 300	ATP6AP2	13; 0	14; 0
chr5:122359566@-	-66; 300	PPIC	13; 0	14; 0
chr1:149876562@-	-93; 300	SV2A	11; 0	14; 0
chr4:148465132@+	-300; 300	EDNRA	9; 0	11; 0
chr3:160219888@-	-51; 300	KPNA4	9; 0	11; 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	39	0.18%	0.61%	82.98%	32	0.975
anti	8	0.04%	0.12%	17.02%	8	0.2
both	47	0.21%	0.73%	100.00%	40	1.175
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	39	0.15%	0.50%	81.25%	32	0.975
anti	9	0.03%	0.11%	18.75%	8	0.225
both	48	0.18%	0.61%	100.00%	40	1.2

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)
chr2:72374990@-	-88; 116	CYP26B1	4; 0	4; 0
chr2:61764828@-	-277; 66	XPO1	3; 0	3; 0
chr4:71588290@+	-290; 89	RUFY3	2; 0	2; 0
chr17:46128423@+	-228; 283	NFE2L1	2; 0	2; 0
chrX:40594663@-	-60; 107	MED14	1; 0	1; 0
chr8:101733810@-	-252; 96	PABPC1	1; 0	1; 0
chr8:38326152@-	-100; 300	FGFR1	0; 1	0; 1
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr7:100200025@+	-113; 74	PCOLCE	1; 0	1; 0
chr6:7542148@+	-171; 85	DSP	0; 1	0; 2

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)
chr2:72374990@-	-88; 116	CYP26B1	4; 0	4; 0
chr2:61764828@-	-277; 66	XPO1	3; 0	3; 0
chr6:7542148@+	-171; 85	DSP	0; 1	0; 2
chr4:71588290@+	-290; 89	RUFY3	2; 0	2; 0
chr17:46128423@+	-228; 283	NFE2L1	2; 0	2; 0
chrX:40594663@-	-60; 107	MED14	1; 0	1; 0
chr8:101733810@-	-252; 96	PABPC1	1; 0	1; 0
chr8:38326152@-	-100; 300	FGFR1	0; 1	0; 1
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr7:100200025@+	-113; 74	PCOLCE	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	41	0.18%	0.64%	35.96%	30	0.455556
anti	73	0.33%	1.14%	64.04%	61	0.811111
both	114	0.51%	1.78%	100.00%	90	1.26667
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	41	0.16%	0.52%	35.04%	30	0.455556
anti	76	0.29%	0.97%	64.96%	61	0.844444
both	117	0.45%	1.49%	100.00%	90	1.3

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)
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr13:41635409@+	-1000; 200	WBP4	0; 5	0; 5
chr20:51588945@+	-1000; 300	TSHZ2	3; 0	3; 0
chr18:29523090@-	-1000; 182	KIAA1012	0; 3	0; 3
chr15:93443418@+	-1000; 300	CHD2	3; 0	3; 0
chr5:55290771@-	-1000; 80	IL6ST	1; 1	1; 1
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr19:37569336@+	-1000; 68	ZNF420	0; 2	0; 2
chr16:89980524@+	-1000; 52	AC092143.1	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)
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr13:41635409@+	-1000; 200	WBP4	0; 5	0; 5
chr20:51588945@+	-1000; 300	TSHZ2	3; 0	3; 0
chr18:29523090@-	-1000; 182	KIAA1012	0; 3	0; 3
chr15:93443418@+	-1000; 300	CHD2	3; 0	3; 0
chr5:55290771@-	-1000; 80	IL6ST	1; 1	1; 1
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr19:37569336@+	-1000; 68	ZNF420	0; 2	0; 2
chr17:70117160@+	-1000; 186	SOX9	0; 1	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 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	1225	5.51%	19.14%	88.96%	664	1.66214
anti	152	0.68%	2.38%	11.04%	75	0.206242
both	1377	6.19%	21.52%	100.00%	737	1.86839
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	1447	5.57%	18.40%	89.27%	664	1.96336
anti	174	0.67%	2.21%	10.73%	75	0.236092
both	1621	6.24%	20.62%	100.00%	737	2.19946

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)
chr2:72356365@-	-300; 1000	CYP26B1	46; 0	81; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 23	0; 28
chr7:100805788@-	-142; 1000	VGF	21; 0	59; 0
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chr2:9628613@-	-300; 1000	ADAM17	14; 0	30; 0
chr19:47278138@-	-300; 1000	SLC1A5	14; 0	14; 0
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 12	0; 13
chr10:102309763@+	-300; 1000	HIF1AN	12; 0	16; 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)
chr2:72356365@-	-300; 1000	CYP26B1	46; 0	81; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	59; 0
chr2:9628613@-	-300; 1000	ADAM17	14; 0	30; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 23	0; 28
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	23; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chr18:40847857@-	-300; 1000	SYT4	11; 0	18; 0
chr12:56555634@-	-300; 1000	SMARCC2	0; 11	0; 18

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	250	1.12%	3.91%	47.08%	81	1.03306
anti	281	1.26%	4.39%	52.92%	162	1.16116
both	531	2.39%	8.30%	100.00%	242	2.19421
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	493	1.90%	6.27%	58.76%	81	2.03719
anti	346	1.33%	4.40%	41.24%	162	1.42975
both	839	3.23%	10.67%	100.00%	242	3.46694

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)
chr1:109642814@+	-1000; 210	snoU2-25	70; 0	267; 0
chrUn_gl000220:109077@+	-758; 300	18S	50; 0	85; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 28	0; 42
chrUn_gl000220:113347@+	-585; 300	28S	28; 0	31; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chrM:5903@+	-162; 300	J01415.8	0; 6	0; 7
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 6	0; 6
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7

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)
chr1:109642814@+	-1000; 210	snoU2-25	70; 0	267; 0
chrUn_gl000220:109077@+	-758; 300	18S	50; 0	85; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 28	0; 42
chrUn_gl000220:113347@+	-585; 300	28S	28; 0	31; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:5903@+	-162; 300	J01415.8	0; 6	0; 7
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 6	0; 6

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	1571	7.06%	24.55%	85.10%	770	1.70575
anti	275	1.24%	4.30%	14.90%	154	0.298588
both	1846	8.30%	28.84%	100.00%	921	2.00434
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	2019	7.78%	25.68%	86.73%	770	2.19218
anti	309	1.19%	3.93%	13.27%	154	0.335505
both	2328	8.97%	29.61%	100.00%	921	2.52769

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)
chr11:65271080@+	-300; 1000	MALAT1	117; 0	291; 0
chrUn_gl000220:110946@+	-300; 539	18S	50; 0	72; 0
chr2:72356365@-	-300; 1000	CYP26B1	46; 0	81; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 23	0; 28
chr17:26880403@-	-300; 372	PIGS	22; 0	26; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	59; 0
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr2:9628613@-	-300; 1000	ADAM17	14; 0	30; 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)
chr11:65271080@+	-300; 1000	MALAT1	117; 0	291; 0
chr2:72356365@-	-300; 1000	CYP26B1	46; 0	81; 0
chrUn_gl000220:110946@+	-300; 539	18S	50; 0	72; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	59; 0
chr2:9628613@-	-300; 1000	ADAM17	14; 0	30; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 23	0; 28
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr17:26880403@-	-300; 372	PIGS	22; 0	26; 0
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 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	423	1.90%	6.61%	89.62%	355	1.06281
anti	49	0.22%	0.77%	10.38%	44	0.123116
both	472	2.12%	7.38%	100.00%	398	1.18593
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	441	1.70%	5.61%	89.09%	355	1.10804
anti	54	0.21%	0.69%	10.91%	44	0.135678
both	495	1.91%	6.30%	100.00%	398	1.24372

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	25; 0	37; 0
chr10:73048078@+	-157; 100	UNC5B	10; 0	11; 0
chr7:90041856@+	-300; 99	CLDN12	4; 0	4; 0
chr6:35715009@+	-300; 26	C6orf81	0; 4	0; 4
chr9:130698280@-	-164; 100	DPM2	3; 0	3; 0
chr2:170668525@-	-141; 100	METTL5	0; 3	0; 3
chr19:42409887@+	-227; 22	ARHGEF1	3; 0	3; 0
chr19:37342559@+	-300; 68	AC008733.3	3; 0	3; 0
chr15:75308869@+	-300; 62	SCAMP5	3; 0	4; 0
chrX:118754079@-	-300; 66	SEPT6	2; 0	2; 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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	25; 0	37; 0
chr10:73048078@+	-157; 100	UNC5B	10; 0	11; 0
chr7:90041856@+	-300; 99	CLDN12	4; 0	4; 0
chr6:35715009@+	-300; 26	C6orf81	0; 4	0; 4
chr15:75308869@+	-300; 62	SCAMP5	3; 0	4; 0
chr9:130698280@-	-164; 100	DPM2	3; 0	3; 0
chr2:170668525@-	-141; 100	METTL5	0; 3	0; 3
chr19:42409887@+	-227; 22	ARHGEF1	3; 0	3; 0
chr19:37342559@+	-300; 68	AC008733.3	3; 0	3; 0
chr11:118108004@-	-300; 30	MPZL3	0; 1	0; 3

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