Parameters
input_file: 20101125_LUjt8_2_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: 14427
[x-link sites] used in any map: 2075 (14.38%)
[single hits (=G+T), cDNA counts] total: 14427
[single hits (=G+T), cDNA counts] used in any map: 2323 (15.44%)

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	608	4.21%	29.30%	624	4.15%	26.86%
intron-exon	-300; 300	495	3.43%	23.86%	506	3.36%	21.78%
5-ncRNA	-1000; 300	247	1.71%	11.90%	317	2.11%	13.65%
ncRNA-3	-300; 1000	257	1.78%	12.39%	390	2.59%	16.79%
ORF-3UTR	-300; 300	65	0.45%	3.13%	67	0.45%	2.88%
5UTR-ORF	-300; 300	13	0.09%	0.63%	14	0.09%	0.60%
inter-5UTR	-1000; 300	48	0.33%	2.31%	48	0.32%	2.07%
3UTR-inter	-300; 1000	121	0.84%	5.83%	123	0.82%	5.29%
inter-5	-1000; 300	196	1.36%	9.45%	261	1.73%	11.24%
3-inter	-300; 1000	303	2.10%	14.60%	436	2.90%	18.77%
BP best in intron	-300; 100	470	3.26%	22.65%	490	3.26%	21.09%

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	563	3.90%	27.13%	92.60%	504	1.0255
anti	45	0.31%	2.17%	7.40%	45	0.0819672
both	608	4.21%	29.30%	100.00%	549	1.10747
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	578	3.84%	24.88%	92.63%	504	1.05282
anti	46	0.31%	1.98%	7.37%	45	0.0837887
both	624	4.15%	26.86%	100.00%	549	1.13661

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)
chr20:329036@+	-47; 300	NRSN2	5; 0	5; 0
chr17:4192523@-	-90; 300	UBE2G1	4; 0	5; 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
chr7:103557520@-	-56; 300	RELN	3; 0	3; 0
chr5:14489178@+	-300; 300	TRIO	3; 0	3; 0
chr3:93699326@+	-135; 300	ARL13B	3; 0	3; 0
chr3:15003999@+	-43; 300	NR2C2	3; 0	3; 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)
chr20:329036@+	-47; 300	NRSN2	5; 0	5; 0
chr17:4192523@-	-90; 300	UBE2G1	4; 0	5; 0
chr1:11140554@-	-207; 300	EXOSC10	4; 0	5; 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
chr7:103557520@-	-56; 300	RELN	3; 0	3; 0
chr5:14489178@+	-300; 300	TRIO	3; 0	3; 0
chr3:93699326@+	-135; 300	ARL13B	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	455	3.15%	21.93%	91.92%	420	0.991285
anti	40	0.28%	1.93%	8.08%	39	0.087146
both	495	3.43%	23.86%	100.00%	459	1.07843
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	466	3.10%	20.06%	92.09%	420	1.01525
anti	40	0.27%	1.72%	7.91%	39	0.087146
both	506	3.36%	21.78%	100.00%	459	1.1024

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)
chr10:43604478@+	-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 (=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)
chr10:43604478@+	-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	143	0.99%	6.89%	57.89%	65	0.899371
anti	104	0.72%	5.01%	42.11%	94	0.654088
both	247	1.71%	11.90%	100.00%	159	1.55346
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	211	1.40%	9.08%	66.56%	65	1.32704
anti	106	0.70%	4.56%	33.44%	94	0.666667
both	317	2.11%	13.65%	100.00%	159	1.99371

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	42; 0	105; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	19; 0	23; 0
chr11:65269806@+	-1000; 29	MALAT1	8; 0	8; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chrUn_gl000220:109077@+	-758; 300	18S	4; 0	4; 0
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

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	42; 0	105; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	19; 0	23; 0
chr11:65269806@+	-1000; 29	MALAT1	8; 0	8; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chrUn_gl000220:109077@+	-758; 300	18S	4; 0	4; 0
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
chrUn_gl000220:113347@+	-585; 300	28S	1; 0	2; 0
chr5:51578400@+	-1000; 146	RP11-668G8.1	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 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	177	1.23%	8.53%	68.87%	71	1.26429
anti	80	0.55%	3.86%	31.13%	70	0.571429
both	257	1.78%	12.39%	100.00%	140	1.83571
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	309	2.05%	13.30%	79.23%	71	2.20714
anti	81	0.54%	3.49%	20.77%	70	0.578571
both	390	2.59%	16.79%	100.00%	140	2.78571

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	100; 0	230; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chrUn_gl000220:110946@+	-300; 539	18S	3; 0	3; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr7:605256@+	-260; 1000	AC147651.5	0; 3	0; 3
chr5:86595502@-	-56; 1000	U6-ENSG00000207452	1; 2	1; 2
chr4:71655925@-	-300; 1000	AC009570.3	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
chr22:19409368@+	-78; 1000	AC000079.1	0; 2	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)
chr11:65271080@+	-300; 1000	MALAT1	100; 0	230; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chrUn_gl000220:110946@+	-300; 539	18S	3; 0	3; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr7:605256@+	-260; 1000	AC147651.5	0; 3	0; 3
chr5:86595502@-	-56; 1000	U6-ENSG00000207452	1; 2	1; 2
chr4:71655925@-	-300; 1000	AC009570.3	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

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	59	0.41%	2.84%	90.77%	55	0.967213
anti	6	0.04%	0.29%	9.23%	6	0.0983607
both	65	0.45%	3.13%	100.00%	61	1.06557
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	61	0.41%	2.63%	91.04%	55	1
anti	6	0.04%	0.26%	8.96%	6	0.0983607
both	67	0.45%	2.88%	100.00%	61	1.09836

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)
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
chr8:27660955@+	-67; 300	ESCO2	0; 1	0; 1
chr7:127222064@-	-300; 300	GCC1	1; 0	1; 0
chr7:92244026@-	-287; 300	CDK6	1; 0	1; 0
chr7:99078924@+	-300; 300	ZNF789	1; 0	1; 0
chr7:44101313@+	-300; 300	DBNL	1; 0	1; 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)
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
chr8:27660955@+	-67; 300	ESCO2	0; 1	0; 1
chr7:127222064@-	-300; 300	GCC1	1; 0	1; 0
chr7:92244026@-	-287; 300	CDK6	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%	0.53%	84.62%	11	0.846154
anti	2	0.01%	0.10%	15.38%	2	0.153846
both	13	0.09%	0.63%	100.00%	13	1
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	11	0.07%	0.47%	78.57%	11	0.846154
anti	3	0.02%	0.13%	21.43%	2	0.230769
both	14	0.09%	0.60%	100.00%	13	1.07692

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)
chr6:7542148@+	-171; 85	DSP	0; 1	0; 2
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

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)
chr6:7542148@+	-171; 85	DSP	0; 1	0; 2
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

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	0.16%	1.11%	47.92%	22	0.511111
anti	25	0.17%	1.20%	52.08%	23	0.555556
both	48	0.33%	2.31%	100.00%	45	1.06667
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	23	0.15%	0.99%	47.92%	22	0.511111
anti	25	0.17%	1.08%	52.08%	23	0.555556
both	48	0.32%	2.07%	100.00%	45	1.06667

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)
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 (=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)
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	100	0.69%	4.82%	82.64%	87	0.934579
anti	21	0.15%	1.01%	17.36%	20	0.196262
both	121	0.84%	5.83%	100.00%	107	1.13084
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	102	0.68%	4.39%	82.93%	87	0.953271
anti	21	0.14%	0.90%	17.07%	20	0.196262
both	123	0.82%	5.29%	100.00%	107	1.14953

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)
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 (=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)
chr17:36890148@-	-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	94	0.65%	4.53%	47.96%	45	0.696296
anti	102	0.71%	4.92%	52.04%	90	0.755556
both	196	1.36%	9.45%	100.00%	135	1.45185
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	158	1.05%	6.80%	60.54%	45	1.17037
anti	103	0.68%	4.43%	39.46%	90	0.762963
both	261	1.73%	11.24%	100.00%	135	1.93333

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	42; 0	105; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chrUn_gl000220:109077@+	-758; 300	18S	4; 0	4; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	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
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

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	42; 0	105; 0
chr20:328867@-	-1000; 62	RP5-1103G7.4	0; 5	0; 5
chrUn_gl000220:109077@+	-758; 300	18S	4; 0	4; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	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
chrUn_gl000220:113347@+	-585; 300	28S	1; 0	2; 0
chr5:140027369@-	-1000; 101	NDUFA2	0; 2	0; 2
chr5:51578400@+	-1000; 146	RP11-668G8.1	0; 1	0; 2
chr21:38739235@+	-1000; 300	DYRK1A	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	232	1.61%	11.18%	76.57%	115	1.31073
anti	71	0.49%	3.42%	23.43%	62	0.40113
both	303	2.10%	14.60%	100.00%	177	1.71186
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	365	2.43%	15.71%	83.72%	115	2.06215
anti	71	0.47%	3.06%	16.28%	62	0.40113
both	436	2.90%	18.77%	100.00%	177	2.46328

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	100; 0	230; 0
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chrUn_gl000220:110946@+	-300; 539	18S	3; 0	3; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr7:605256@+	-260; 1000	AC147651.5	0; 3	0; 3
chr4:71655925@-	-300; 1000	AC009570.3	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

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	100; 0	230; 0
chr17:36890148@-	-300; 988	PCGF2	6; 0	6; 0
chr3:39256163@+	-237; 1000	RP11-331G2.4	4; 0	4; 0
chrUn_gl000220:110946@+	-300; 539	18S	3; 0	3; 0
chr9:14205038@+	-300; 1000	RP11-280O24.3	0; 3	0; 3
chr7:605256@+	-260; 1000	AC147651.5	0; 3	0; 3
chr4:71655925@-	-300; 1000	AC009570.3	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

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	442	3.06%	21.30%	94.04%	400	1.03513
anti	28	0.19%	1.35%	5.96%	27	0.0655738
both	470	3.26%	22.65%	100.00%	427	1.1007
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	461	3.06%	19.85%	94.08%	400	1.07963
anti	29	0.19%	1.25%	5.92%	27	0.0679157
both	490	3.26%	21.09%	100.00%	427	1.14754

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	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
chr7:157174488@+	-300; 100	DNAJB6	2; 0	2; 0
chr6:105220056@-	-300; 100	HACE1	2; 0	2; 0
chr5:154214515@-	-300; 22	C5orf4	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	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
chr9:106899892@+	-300; 100	SMC2	1; 0	2; 0
chr9:36210576@+	-300; 43	CLTA	1; 0	2; 0
chr8:53536534@-	-300; 100	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.