Spreadsheet: b23f5f57-7528-46ee-afe8-6210e4665d83
Sheet: Sheet1

Table S1A. Full Mapping Stats | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20
 | UHR120 F3 (forward) |  | UHR120 F5  (reverse) |  | UHR150 F3 |  | UHR150 F5 |  | HBR120 F3 |  | HBR120 F5 |  | HBR150 F3 |  | HBR150 F5 |  | MCF7 F3 |  | MCF7 F5
Total Reads: | 175839941 | -1 | 173593017 | -1 | 212899838 | -1 | 217864708 | -1 | 200578721 | -1 | 197995799 | -1 | 241409833 | -1 | 247031687 | -1 | 360318799 | -1 | 364115004 | -1
Reads mapped regular reference | 94302044 | -0.536 | 48637153 | -0.28 | 133502911 | -0.627 | 96601901 | -0.443 | 102272963 | -0.51 | 54883162 | -0.277 | 148100495 | -0.613 | 108142810 | -0.438 | 250576238 | -0.695 | 127163654 | -0.349
Reads mapped with rescue | 802726 | -0.005 | 11792055 | -0.068 | 1177127 | -0.006 | 13167662 | -0.06 | 801882 | -0.004 | 11291828 | -0.057 | 1237391 | -0.005 | 13265367 | -0.054 | 1021063 | -0.003 | 27321013 | -0.075
Reads mapped total | 95060185 | -0.541 | 60245606 | -0.347 | 134569252 | -0.632 | 109357663 | -0.502 | 103038107 | -0.514 | 66039318 | -0.334 | 149240829 | -0.618 | 121109768 | -0.49 | 251455643 | -0.698 | 153965357 | -0.423
Reads filtered: | 13978518 | -0.079 | 8881529 | -0.051 | 14672001 | -0.069 | 12641033 | -0.058 | 17909340 | -0.089 | 12144462 | -0.061 | 17820548 | -0.074 | 16814988 | -0.068 | 7635031 | -0.021 | 2614408 | -0.007
Table S1B. UHR and HBR barcoded runs mapping, splicing and fusion stats with PE 1+ SR 1+.
Barcode | Sample | Type | [NAME] | Reads | Mapped | Unique | Known-Junction | Putative-Junction
B-1 | UHR | Paired End | 150 | 37752922 | 26489739 | 19844542 | 100443 | 3466
B-2 | UHR | Paired End | 150 | 38051535 | 27557161 | 20714906 | 100418 | 3535
B-3 | UHR | Paired End | 250 | 35666384 | 24965296 | 17877867 | 88557 | 2672
B-4 | UHR | Paired End | 250 | 32947777 | 22569912 | 16386154 | 85923 | 2472
B-5 | UHR | Paired End | 100 to 300 | 35530359 | 24737248 | 18558042 | 99921 | 3317
B-6 | UHR | Paired End | 100 to 300 | 37915731 | 26247505 | 19765990 | 100662 | 3442
B-1 + B-2 | UHR | Paired End | 150 | 75804457 | 54046900 | 40559448 | 117558 | 6296
B-3 + B-4 | UHR | Paired End | 250 | 68614161 | 47535208 | 34264021 | 106641 | 4876
B-5 + B-6 | UHR | Paired End | 100 to 300 | 73446090 | 50984753 | 38324032 | 117620 | 6121
B-all (1 to 6) | UHR | Paired End | All | 217864708 | 152566861 | 113147501 | 136671 | 14271
B-7 | HBR | Paired End | 150 | 45033309 | 30806883 | 23910296 | 100676 | 3542
B-8 | HBR | Paired End | 150 | 40501541 | 28343720 | 21950374 | 99007 | 3317
[NAME] | HBR | Paired End | 250 | 38537408 | 25997484 | 19502635 | 86402 | 2730
B-10 | HBR | Paired End | 250 | 34113430 | 23701380 | 17469189 | 83547 | 2462
B-11 | HBR | Paired End | 100 to 300 | 45645740 | 31510238 | 24464205 | 102346 | 3790
B-12 | HBR | Paired End | 100 to 300 | 43200259 | 29409864 | 22653367 | 99606 | 3454
[NAME] | HBR | Paired End | 150 | 85534850 | 59150603 | 45860670 | 118230 | 6038
[NAME] | HBR | Paired End | 250 | 72650838 | 49698864 | 36971824 | 105810 | 4809
B-11 + B-12 | HBR | Paired End | 100 to 300 | 88845999 | 60920102 | 47117572 | 119355 | 6440
B-all (7 to 12) | HBR | Paired End | All | 247031687 | 169769569 | 129950066 | 138536 | 14083
Table S1C. UHR and HBR barcoded runs mapping, splicing and fusion stats with SR 1+
Barcode | Sample | Type | [NAME] | Reads | Mapped | Unique | Known-Junction | Putative-Junction
B-1 | UHR | Single Read 1+ | 150 | 36884871 | 25159156 | 16300575 | 109563 | 18571
B-2 | UHR | Single Read 1+ | 150 | 37187279 | 25997524 | 17178135 | 108388 | 17370
B-3 | UHR | Single Read 1+ | 250 | 34860731 | 23488345 | 15135073 | 101989 | 16542
B-4 | UHR | Single Read 1+ | 250 | 32197142 | 21281148 | 13769470 | 99900 | 15408
B-5 | UHR | Single Read 1+ | 100 to 300 | 34718441 | 23591090 | 15107112 | 111348 | 18971
B-6 | UHR | Single Read 1+ | 100 to 300 | 37051374 | 25020966 | 16247801 | 108860 | 17336
B-1 + B-2 | UHR | Single Read 1+ | 150 | 74072150 | 51156680 | 33478710 | 126120 | 33386
B-3 + B-4 | UHR | Single Read 1+ | 250 | 67057873 | 44769493 | 28904543 | 119510 | 29946
B-5 + B-6 | UHR | Single Read 1+ | 100 to 300 | 71769815 | 48612056 | 31354913 | 127110 | 33685
B-all (1 to 6) | UHR | Single Read 1+ | All | 212899838 | 144538229 | 93738166 | 144106 | 89547
B-7 | HBR | Single Read 1+ | 150 | 44003009 | 29489712 | 19884394 | 109713 | 18815
B-8 | HBR | Single Read 1+ | 150 | 39578339 | 27142069 | 18382111 | 109336 | 18872
[NAME] | HBR | Single Read 1+ | 250 | 37661403 | 24645516 | 16570910 | 104918 | 17544
B-10 | HBR | Single Read 1+ | 250 | 33334349 | 22407220 | 14454558 | 101167 | 16198
B-11 | HBR | Single Read 1+ | 100 to 300 | 44610571 | 30382449 | 20491536 | 109049 | 17800
B-12 | HBR | Single Read 1+ | 100 to 300 | 42222161 | 27967246 | 18652756 | 109891 | 18644
[NAME] | HBR | Single Read 1+ | 150 | 83581348 | 56631781 | 38266505 | 125491 | 35166
[NAME] | HBR | Single Read 1+ | 250 | 70995752 | 47052736 | 31025468 | 120276 | 31783
B-11 + B-12 | HBR | Single Read 1+ | 100 to 300 | 86832732 | 58349695 | 39144292 | 125455 | 34059
B-all (7 to 12) | HBR | Single Read 1+ | All | 241409832 | 162034212 | 108436265 | 145629 | 85622
Table S1D. UHR and HBR barcoded runs mapping, splicing and fusion stats with SR 2+
Barcode | Sample | Type | [NAME] | Reads | Mapped | Unique | Known-Junction | Putative-Junction
B-1 | UHR | Single Read | 150 | 36884871 | 25159156 | 16300575 | 81005 | 1236
B-2 | UHR | Single Read | 150 | 37187279 | 25997524 | 17178135 | 80541 | 1277
B-3 | UHR | Single Read | 250 | 34860731 | 23488345 | 15135073 | 74665 | 1065
B-4 | UHR | Single Read | 250 | 32197142 | 21281148 | 13769470 | 70331 | 930
B-5 | UHR | Single Read | 100 to 300 | 34718441 | 23591090 | 15107112 | 79302 | 1150
B-6 | UHR | Single Read | 100 to 300 | 37051374 | 25020966 | 16247801 | 80797 | 1226
B-1 + B-2 | UHR | Single Read | 150 | 74072150 | 51156680 | 33478710 | 101752 | 2681
B-3 + B-4 | UHR | Single Read | 250 | 67057873 | 44769493 | 28904543 | 94575 | 2116
B-5 + B-6 | UHR | Single Read | 100 to 300 | 71769815 | 48612056 | 31354913 | 101601 | 2515
B-all (1 to 6) | UHR | Single Read | All | 212899838 | 144538229 | 93738166 | 126603 | 7625
B-7 | HBR | Single Read | 150 | 44003009 | 29489712 | 19884394 | 78510 | 1401
B-8 | HBR | Single Read | 150 | 39578339 | 27142069 | 18382111 | 77263 | 1341
[NAME] | HBR | Single Read | 250 | 37661403 | 24645516 | 16570910 | 69979 | 1080
B-10 | HBR | Single Read | 250 | 33334349 | 22407220 | 14454558 | 66764 | 939
B-11 | HBR | Single Read | 100 to 300 | 44610571 | 30382449 | 20491536 | 81216 | 1452
B-12 | HBR | Single Read | 100 to 300 | 42222161 | 27967246 | 18652756 | 77869 | 1263
[NAME] | HBR | Single Read | 150 | 83581348 | 56631781 | 38266505 | 100453 | 2798
[NAME] | HBR | Single Read | 250 | 70995752 | 47052736 | 31025468 | 91550 | 2165
B-11 + B-12 | HBR | Single Read | 100 to 300 | 86832732 | 58349695 | 39144292 | 101943 | 2791
B-all (7 to 12) | HBR | Single Read | All | 241409832 | 162034212 | 108436265 | 127614 | 7836
Table S1E. Tophat vs Lifescope mapping performance using [NAME] with MCF7-1 dataset.
 | Tophat 1.3.0 | Lifescope 2.0
Total* | 124236156 | 540187060
Mapped | 124236156 | 404901929
Paired | 94035704 | 540187060
Read1 | 63835252 | 270093530
Read2 | 53097549 | 270093530
Proper Paired | 33634800 | 158050096
Mate and read mapped | 30200452 | 269616798
Singletons | 25777986 | 135285131
Different Chr | 0 | 104560670
Different Chr MapQ>5 | 0 | 49603712
*Tophat reports only mapped reads in BAM file whereas Lifescope reports both mapped and unmapped reads. Same set of reads were used for both analyses