samples NAME
1 002-002 CCDC91--CD47
2 002-002 PGD--GK
3 002-002 DSTN--PCSK2
4 002-002 MANBAL--RRBP1
5 002-002 IGKV4-1--IGKJ4
6 002-002 KDM4C--HERC3
NREAD_SPANS NREAD_JXNLEFT NREAD_JXNRIGHT FUSION_CLASS
1 0 0 2 TRANSLOCATION
2 0 0 3 TRANSLOCATION
3 1 0 2 READ_THROUGH
4 0 2 0 INTERCHROM_INTERSTRAND
5 9 3 3 READ_THROUGH
6 0 0 2 TRANSLOCATION
SPLICE_TYPE BRKPT_LEFT BRKPT_RIGHT LEFT_SYMBOL
1 CANONICAL_SPLICING chr12:28515447:+ chr3:107779698:- CCDC91
2 CANONICAL_SPLICING chr1:10460628:+ chrX:30742217:+ PGD
3 CANONICAL_SPLICING chr20:17550855:+ chr20:17389907:+ DSTN
4 CANONICAL_SPLICING chr20:35929815:+ chr20:17641172:- MANBAL
5 NON-CANONICAL_SPLICING chr2:89185666:+ chr2:89160432:- IGKV4-1
6 CANONICAL_SPLICING chr9:6893231:+ chr4:89607886:+ KDM4C
RIGHT_SYMBOL ANNOT_FORMAT
1 CD47 Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
2 GK Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
3 PCSK2 Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
4 RRBP1 Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
5 IGKJ4 Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
6 HERC3 Symbol:Transcript:Strand:Exon_No:Dist_to_Exon:Frame:CDS_Length
LEFT_ANNOT
1 CCDC91:ENST00000381259.5_1:+:6:0:0:291958,CCDC91:ENST00000539107.5_2:+:7:0:0:291958,CCDC91:ENST00000545336.5_1:+:10:0:0:291958,CCDC91:ENST00000545737.5_1:+:6:0:0:195425,CCDC91:ENST00000536442.5_1:+:7:0:0:195421,CCDC91:ENST00000543809.5_1:+:7:0:0:155580,CCDC91:ENST00000535520.5_1:+:9:0:-1:47469,CCDC91:ENST00000539904.1_1:+:6:0:-1:0,CCDC91:ENST00000540401.5_1:+:6:0:-1:0,CCDC91:ENST00000540794.5_1:+:NA:NA:NA:268730,CCDC91:ENST00000536154.5_1:+:NA:NA:NA:33932
2 PGD:ENST00000270776.13_2:+:3:0:0:20632,PGD:ENST00000460189.1_1:+:2:0:0:13620,PGD:ENST00000491493.5_3:+:3:0:0:11893,PGD:ENST00000465632.5_1:+:2:0:0:8481,PGD:ENST00000477958.5_1:+:3:0:0:1366,PGD:ENST00000483936.5_1:+:NA:NA:NA:18392
3 DSTN:ENST00000246069.12_2:+:1:0:0:36938,DSTN:ENST00000449141.2_1:+:1:0:0:34921,DSTN:ENST00000474024.5_1:+:1:0:-1:6361
4 MANBAL:ENST00000373605.7_1:+:3:0:0:15152,MANBAL:ENST00000373606.7_1:+:2:0:0:15152,MANBAL:ENST00000397151.1_1:+:3:0:0:15152,MANBAL:ENST00000397152.7_1:+:4:0:0:15152,MANBAL:ENST00000397150.5_1:+:2:0:0:1037
5 IGKV4-1:ENST00000390243.2_2:+:2:2:1:582
6 KDM4C:ENST00000381309.7_3:+:8:0:0:381741,KDM4C:ENST00000381306.7_3:+:8:0:0:377052,KDM4C:ENST00000536108.5_2:+:8:0:0:355503,KDM4C:ENST00000543771.5_2:+:8:0:0:283463,KDM4C:ENST00000438023.5_2:+:8:0:0:188860,KDM4C:ENST00000496464.1_1:+:1:0:-1:0,KDM4C:ENST00000489243.5_1:+:8:400:-1:0
RIGHT_ANNOT
1 CD47:ENST00000355354.13_3:-:4:0:1:43625,CD47:ENST00000361309.5_2:-:4:0:1:43621,CD47:ENST00000644850.1_1:-:4:0:1:20799
2 GK:ENST00000378943.7_2:+:18:0:1:75205,GK:ENST00000378945.7_2:+:18:0:1:75205,GK:ENST00000378946.7_1:+:19:0:1:75205,GK:ENST00000427190.5_2:+:19:0:1:75205,GK:ENST00000481024.5_1:+:20:0:-1:20814,GK-AS1:ENST00000464659.1_1:-:1:74:-1:0
3 PCSK2:ENST00000262545.7_2:+:6:0:0:254765,PCSK2:ENST00000536609.1_1:+:5:0:0:254765,PCSK2:ENST00000377899.5_1:+:7:0:0:254708,PCSK2:ENST00000470007.1_1:+:6:0:-1:0
4 RRBP1:ENST00000360807.8_3:-:2:0:0:46326,RRBP1:ENST00000377807.6_3:-:3:0:0:46326,RRBP1:ENST00000377813.5_3:-:3:0:0:46326,RRBP1:ENST00000398782.2_5:-:2:0:0:902,RRBP1:ENST00000455029.3_1:-:NA:NA:NA:28881
5 IGKJ4:ENST00000390239.2_3:-:1:1:0:37,AC244205.1:ENST00000624935.3_2:-:NA:NA:NA:0
6 HERC3:ENST00000264345.7_1:+:20:0:2:101137,HERC3:ENST00000402738.6_3:+:22:0:2:101137,HERC3:ENST00000512194.1_1:+:6:0:2:17161
DISTANCE
1 NA
2 NA
3 160950
4 18288643
5 25234
6 NA
ASSEMBLED_CONTIGS
1 GGATCTATATTTAAGTGCTTATATTCATCCACAATAATGCTGAGGGCTTCG
2 GGGCAAGCTGTGGATGATTTCATCGAGAAATTGAAAGTGAAATTCGTTATT,AAGTGGTATTCCATAAAACCTACCAACTCATGGATTCCCAAGATGTGAGCT
3 CCTGCGACCGCCGCGGCGAAGATGAATGCCGAAGCAAGTTACGACTTCAGCAGCAACGACCCCTATCCTTACCCTCG
4 GGACTCTTCCTGGGAGCCATCTTCCAGCTCATCTGTGTGCTGGCCATCATC
5 GGCCTCTCTGGGATAGAAGTTATTCAGCAGGCACACAACAGAGGCAGTTCCAGATTTCAACTGCTCATCAGATGGCGGGAAGATGAAGACAGATGGTGCAGCCACAGTTCGTTTGATCTCCACCTTGGTCCCTCCGCCGAAAGTGAGAGTATTATAATATTGCTGACAGTAATAAACTGCCACATCTTCAGCCTGCAGGCTGCTGATGGTGAGAG
6 GATTGACTATGGAAAAGTTGCCAAATTGGAGTCTCCAAGAGCTTTTAGAT,ATCTGCCGAGAAAGCTATGGAGTGATTGAACAGAAGAAGCTGATACCTGGG
ASSEMBLY_CROSS_JXN PRIMERS
1 TRUE AGGAAAGCTGGTCACGAAGC,CCTGGGACGAAAAGAATGGC
2 TRUE TGGGCAAGCTGTGGATGATT,AGCTCACATCTTGGGAATCCA
3 TRUE GAGGACGGTCTGCATACTCG,TCGTTGCTGCTGAAGTCGTA
4 FALSE ACTCTTCCTGGGAGCCATCT,AAAGACCACAACCCCCAAGG
5 TRUE TCACTCTCACCATCAGCAGC,TGATCTCCACCTTGGTCCCT
6 TRUE CAAGATAACCCAGGAGGCTGG,AGTCTCCTCCACATCCTCCC
ID SPAN_CROSSHOM_SCORE JXN_CROSSHOM_SCORE
1 chr12:28515449:+:chr3:107779700:-:4:0 0 0
2 chr1:10460630:+:chrX:30742217:+:1:0 0 0
3 chr20:17550857:+:chr20:17389907:+:1:0 0 0
4 chr20:35929817:+:chr20:17641174:-:1:4 0 0
5 chr2:89185668:+:chr2:89160434:-:1:0 0 0
6 chr9:6893233:+:chr4:89607886:+:1:1 0 0
OVERHANG_DIVERSITY MINFRAG20 MINFRAG35 OVERHANG_MEANBQ SPAN_MEANBQ JXN_MEANBQ
1 1 1 0 38.50000 NA 38.75000
2 2 2 0 37.33333 NA 38.00000
3 2 2 0 37.50000 38.50000 36.75000
4 2 2 0 39.00000 NA 39.25000
5 3 3 1 31.66667 37.22222 29.83333
6 1 1 0 36.00000 NA 38.25000
OVERHANG_BQ15 SPAN_BQ15 JXN_BQ15 OVERHANG_MM SPAN_MM JXN_MM
1 2 0 4 0 NA 0.0000000
2 3 0 6 0 NA 0.3333333
3 2 2 4 0 0.5000000 0.0000000
4 2 0 4 0 NA 0.0000000
5 6 18 12 1 0.4444444 0.0000000
6 2 0 4 0 NA 0.0000000
OVERHANG_MEANLEN SPAN_MEANLEN JXN_MEANLEN TPM_FUSION TPM_LEFT TPM_RIGHT
1 34.00000 NA 34.00000 7.333199 6.400550 58.733329
2 32.66667 NA 33.83333 4.518474 14.731858 14.385095
3 23.50000 41.50000 39.25000 8.130358 248.322240 20.247429
4 33.00000 NA 34.00000 111.009156 31.226601 6.077102
5 32.33333 49.33333 30.33333 21.386369 13.404606 110.877316
6 28.00000 NA 36.75000 28.077132 8.035374 12.548261
MAX_TRX_FUSION DISPOSITION
1 ENST00000381259.5_1--ENST00000644850.1_1|670 PASS
2 ENST00000270776.13_2--ENST00000378945.7_2|318 PASS
3 ENST00000246069.12_2--ENST00000470007.1_1|137 PASS
4 ENST00000397150.5_1--ENST00000398782.2_5|244 PASS
5 ENST00000390243.2_2--ENST00000390239.2_3|536 PASS
6 ENST00000543771.5_2--ENST00000512194.1_1|999 PASS
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)
Matrix products: default
BLAS/LAPACK: /mounts/isilon/data/eahome/u1072932/anaconda3/envs/r-4.0.3/lib/libopenblasp-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] writexl_1.3.1 readxl_1.3.1 forcats_0.5.0 stringr_1.4.0
[5] dplyr_1.0.7 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2
[9] tibble_3.1.2 ggplot2_3.3.5 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 cellranger_1.1.0 pillar_1.6.1 compiler_4.0.3
[5] dbplyr_2.1.1 tools_4.0.3 jsonlite_1.7.2 lubridate_1.7.9.2
[9] lifecycle_1.0.0 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
[13] reprex_0.3.0 cli_3.0.0 rstudioapi_0.13 DBI_1.1.1
[17] haven_2.3.1 withr_2.4.2 xml2_1.3.2 httr_1.4.2
[21] fs_1.5.0 generics_0.1.0 vctrs_0.3.8 hms_1.1.0
[25] grid_4.0.3 tidyselect_1.1.1 glue_1.4.2 R6_2.5.0
[29] fansi_0.5.0 modelr_0.1.8 magrittr_2.0.1 backports_1.2.1
[33] scales_1.1.1 ellipsis_0.3.2 rvest_0.3.6 assertthat_0.2.1
[37] colorspace_2.0-2 utf8_1.2.1 stringi_1.6.2 munsell_0.5.0
[41] broom_0.7.5 crayon_1.4.1
We are using STAR-SEQR for fusion detection and I am trying to visualize the data using chimeraviz. Is there a good way to input the STAR-SEQR's output? Below is some information about the data and sessionInfo():