CeGaT Fusion Detection Software Package<\/p>\n<\/div><\/div><\/div>
This software is intended to call fusion and exon-skipping events from raw sequencing data generated from human samples using the Twist Alliance CeGaT RNA Fusion Panel<\/a> and sequenced on Illumina HiSeq\/NovaSeq\u2122 systems. Note that this software is not intended for installation on personal computers, and does not offer a graphical user interface. It is intended to be run as part of bioinformatics pipelines on compute infrastructure, and its output files will need to be post-processed for interpretation by non-technical users.<\/p>\nIf you are looking for cancer diagnostics as a service, please visit our diagnostic pages here<\/a>. If you are interested in sequencing services, please have a look here<\/a>.<\/p>\nBackground<\/h4>\nFusion detection involves multiple steps that are performed automatically by our software package: First, reads are aligned using the STAR aligner (Dobin et al, Bioinformatics 2013) to the human reference genome hg19. After a first mapping pass, identified novel splice sites are integrated into the reference and a second pass mapping is performed. The resulting read alignments are analyzed by STARfusion (Haas et al, Genome Biol 2019) to detect fusion transcripts. We post-process the STARfusion output to correct for varying levels of read duplication, filter fusion calls to the intended panel target regions, and scan for transcript variants (e.g., MET exon 14 skipping) which STARfusion does not detect.<\/p>\n<\/div><\/div><\/div>Contact us<\/span><\/a><\/div><\/div><\/div><\/div>Downloads<\/span><\/a><\/div><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>Steps How to Use the Software<\/h2><\/div>Step 1<\/a><\/h4><\/div>Installation<\/p>\n<\/div><\/div><\/div>Step 2<\/a><\/h4><\/div>Sequencing Data<\/p>\n<\/div><\/div><\/div>Step 3<\/a><\/h4><\/div>Running the application<\/p>\n<\/div><\/div><\/div>Step 4<\/a><\/h4><\/div>Result files<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>Installation<\/h2><\/div><\/div>We distribute the software as containerized application. To run it, an OCI compatible runtime environment is needed, such as docker.<\/p>\nTo setup docker, please refer to the online documentation here<\/a>.<\/p>\n\nDownload the container image from here<\/a>. The download is 31 GB in size.<\/li>\nInstall the image by calling docker load <cegat_starfusion.dockerimage<\/span><\/li>\nDownload the wrapper script<\/a>.<\/li>\n<\/ul>\n<\/div><\/div><\/div>Sequencing Data<\/h2><\/div><\/div>The process of generating sequencing data should follow roughly these steps:<\/p>\n\nRNA extraction from a suitable sample<\/li>\nSequencing library preparation using a strand-specific protocol (e.g. using the Twist RNA library prep)<\/li>\nTarget Enrichment using the Twist workflow and the Twist Alliance CeGaT RNA Fusion Panel<\/a><\/li>\nSequencing on an Illumina instrument generating paired-end reads of at least 100+100 bp<\/li>\n<\/ul>\n<\/div><\/div><\/div>Running the Application<\/h2><\/div><\/div>The input files to the application are fastq files generated by the sequencer. You will need two files per sample, one for the forward reads and one for the reverse reads. These must be in fastq.gz format. Adapter trimming should be performed before running the fusion detection.<\/p>\n\nPrepare an empty output folder for your results, let’s say \/path\/results<\/span><\/li>\nSelect your sequencing data files, say \/path\/mysample.1.fastq.gz<\/span> and \/path\/mysample.2.fastq.gz<\/span><\/li>\nDecide on how many CPU cores the analysis should use. If you are unsure, you can call the command: nproc<\/span>\nFor this example, let’s assume the command returns “64” and you want to use all available cores.<\/li>\nStart the process: bash wrapper.sh \/path\/mysample.1.fastq.gz \/path\/mysample.2.fastq.gz \/path\/result 64<\/span><\/li>\n<\/ul>\n<\/div><\/div><\/div>Result Files<\/h2><\/div>All output files are tab-separated tabular text files. All coordinates are given on the hg19 reference genome.<\/p>\nThe main output file is combined_results.tsv<\/span><\/p>\nIt is a two-column tab-separated file:\n<\/strong>(1) Event Name, e.g. ALK\u2013EML4 or EGFR_vIII\n(2) FFPM, the number of fragments per million supporting this event. FFPM is the count of the number of reads supporting this fusion events, normalized by the total number of unique molecules that were sequenced.<\/p>\nNote: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
If you are looking for cancer diagnostics as a service, please visit our diagnostic pages here<\/a>. If you are interested in sequencing services, please have a look here<\/a>.<\/p>\nBackground<\/h4>\nFusion detection involves multiple steps that are performed automatically by our software package: First, reads are aligned using the STAR aligner (Dobin et al, Bioinformatics 2013) to the human reference genome hg19. After a first mapping pass, identified novel splice sites are integrated into the reference and a second pass mapping is performed. The resulting read alignments are analyzed by STARfusion (Haas et al, Genome Biol 2019) to detect fusion transcripts. We post-process the STARfusion output to correct for varying levels of read duplication, filter fusion calls to the intended panel target regions, and scan for transcript variants (e.g., MET exon 14 skipping) which STARfusion does not detect.<\/p>\n<\/div><\/div><\/div>Contact us<\/span><\/a><\/div><\/div><\/div><\/div>Downloads<\/span><\/a><\/div><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/span><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>Steps How to Use the Software<\/h2><\/div>Step 1<\/a><\/h4><\/div>Installation<\/p>\n<\/div><\/div><\/div>Step 2<\/a><\/h4><\/div>Sequencing Data<\/p>\n<\/div><\/div><\/div>Step 3<\/a><\/h4><\/div>Running the application<\/p>\n<\/div><\/div><\/div>Step 4<\/a><\/h4><\/div>Result files<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>Installation<\/h2><\/div><\/div>We distribute the software as containerized application. To run it, an OCI compatible runtime environment is needed, such as docker.<\/p>\nTo setup docker, please refer to the online documentation here<\/a>.<\/p>\n\nDownload the container image from here<\/a>. The download is 31 GB in size.<\/li>\nInstall the image by calling docker load <cegat_starfusion.dockerimage<\/span><\/li>\nDownload the wrapper script<\/a>.<\/li>\n<\/ul>\n<\/div><\/div><\/div>Sequencing Data<\/h2><\/div><\/div>The process of generating sequencing data should follow roughly these steps:<\/p>\n\nRNA extraction from a suitable sample<\/li>\nSequencing library preparation using a strand-specific protocol (e.g. using the Twist RNA library prep)<\/li>\nTarget Enrichment using the Twist workflow and the Twist Alliance CeGaT RNA Fusion Panel<\/a><\/li>\nSequencing on an Illumina instrument generating paired-end reads of at least 100+100 bp<\/li>\n<\/ul>\n<\/div><\/div><\/div>Running the Application<\/h2><\/div><\/div>The input files to the application are fastq files generated by the sequencer. You will need two files per sample, one for the forward reads and one for the reverse reads. These must be in fastq.gz format. Adapter trimming should be performed before running the fusion detection.<\/p>\n\nPrepare an empty output folder for your results, let’s say \/path\/results<\/span><\/li>\nSelect your sequencing data files, say \/path\/mysample.1.fastq.gz<\/span> and \/path\/mysample.2.fastq.gz<\/span><\/li>\nDecide on how many CPU cores the analysis should use. If you are unsure, you can call the command: nproc<\/span>\nFor this example, let’s assume the command returns “64” and you want to use all available cores.<\/li>\nStart the process: bash wrapper.sh \/path\/mysample.1.fastq.gz \/path\/mysample.2.fastq.gz \/path\/result 64<\/span><\/li>\n<\/ul>\n<\/div><\/div><\/div>Result Files<\/h2><\/div>All output files are tab-separated tabular text files. All coordinates are given on the hg19 reference genome.<\/p>\nThe main output file is combined_results.tsv<\/span><\/p>\nIt is a two-column tab-separated file:\n<\/strong>(1) Event Name, e.g. ALK\u2013EML4 or EGFR_vIII\n(2) FFPM, the number of fragments per million supporting this event. FFPM is the count of the number of reads supporting this fusion events, normalized by the total number of unique molecules that were sequenced.<\/p>\nNote: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
Fusion detection involves multiple steps that are performed automatically by our software package: First, reads are aligned using the STAR aligner (Dobin et al, Bioinformatics 2013) to the human reference genome hg19. After a first mapping pass, identified novel splice sites are integrated into the reference and a second pass mapping is performed. The resulting read alignments are analyzed by STARfusion (Haas et al, Genome Biol 2019) to detect fusion transcripts. We post-process the STARfusion output to correct for varying levels of read duplication, filter fusion calls to the intended panel target regions, and scan for transcript variants (e.g., MET exon 14 skipping) which STARfusion does not detect.<\/p>\n<\/div><\/div><\/div>
Installation<\/p>\n<\/div><\/div><\/div>
Sequencing Data<\/p>\n<\/div><\/div><\/div>
Running the application<\/p>\n<\/div><\/div><\/div>
Result files<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>
We distribute the software as containerized application. To run it, an OCI compatible runtime environment is needed, such as docker.<\/p>\n
To setup docker, please refer to the online documentation here<\/a>.<\/p>\n\nDownload the container image from here<\/a>. The download is 31 GB in size.<\/li>\nInstall the image by calling docker load <cegat_starfusion.dockerimage<\/span><\/li>\nDownload the wrapper script<\/a>.<\/li>\n<\/ul>\n<\/div><\/div><\/div>Sequencing Data<\/h2><\/div><\/div>The process of generating sequencing data should follow roughly these steps:<\/p>\n\nRNA extraction from a suitable sample<\/li>\nSequencing library preparation using a strand-specific protocol (e.g. using the Twist RNA library prep)<\/li>\nTarget Enrichment using the Twist workflow and the Twist Alliance CeGaT RNA Fusion Panel<\/a><\/li>\nSequencing on an Illumina instrument generating paired-end reads of at least 100+100 bp<\/li>\n<\/ul>\n<\/div><\/div><\/div>Running the Application<\/h2><\/div><\/div>The input files to the application are fastq files generated by the sequencer. You will need two files per sample, one for the forward reads and one for the reverse reads. These must be in fastq.gz format. Adapter trimming should be performed before running the fusion detection.<\/p>\n\nPrepare an empty output folder for your results, let’s say \/path\/results<\/span><\/li>\nSelect your sequencing data files, say \/path\/mysample.1.fastq.gz<\/span> and \/path\/mysample.2.fastq.gz<\/span><\/li>\nDecide on how many CPU cores the analysis should use. If you are unsure, you can call the command: nproc<\/span>\nFor this example, let’s assume the command returns “64” and you want to use all available cores.<\/li>\nStart the process: bash wrapper.sh \/path\/mysample.1.fastq.gz \/path\/mysample.2.fastq.gz \/path\/result 64<\/span><\/li>\n<\/ul>\n<\/div><\/div><\/div>Result Files<\/h2><\/div>All output files are tab-separated tabular text files. All coordinates are given on the hg19 reference genome.<\/p>\nThe main output file is combined_results.tsv<\/span><\/p>\nIt is a two-column tab-separated file:\n<\/strong>(1) Event Name, e.g. ALK\u2013EML4 or EGFR_vIII\n(2) FFPM, the number of fragments per million supporting this event. FFPM is the count of the number of reads supporting this fusion events, normalized by the total number of unique molecules that were sequenced.<\/p>\nNote: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
The process of generating sequencing data should follow roughly these steps:<\/p>\n
The input files to the application are fastq files generated by the sequencer. You will need two files per sample, one for the forward reads and one for the reverse reads. These must be in fastq.gz format. Adapter trimming should be performed before running the fusion detection.<\/p>\n
All output files are tab-separated tabular text files. All coordinates are given on the hg19 reference genome.<\/p>\n
The main output file is combined_results.tsv<\/span><\/p>\nIt is a two-column tab-separated file:\n<\/strong>(1) Event Name, e.g. ALK\u2013EML4 or EGFR_vIII\n(2) FFPM, the number of fragments per million supporting this event. FFPM is the count of the number of reads supporting this fusion events, normalized by the total number of unique molecules that were sequenced.<\/p>\nNote: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
It is a two-column tab-separated file:\n<\/strong>(1) Event Name, e.g. ALK\u2013EML4 or EGFR_vIII\n(2) FFPM, the number of fragments per million supporting this event. FFPM is the count of the number of reads supporting this fusion events, normalized by the total number of unique molecules that were sequenced.<\/p>\nNote: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
Note: <\/strong>Reporting is limited to the transcript variants listed below, and to fusions involving one of the genes listed.<\/p>\n<\/div><\/i><\/i><\/span>Gene list for de-novo fusion detection<\/span><\/a><\/h6><\/div>\nABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
ABL1, ACTB, AFAP1, AGK, AKAP4, AKAP9, AKAP12, AKT1, AKT2, AKT3, ALK, ARHGAP6, ARHGAP26, ASPL, ASPSCR1, ATF1, ATP1B1, ATRX, AVIL, AXL, BAG4, BCL2, BCOR, BCORL1, BCR, BEND2, BICC1, BRAF, BRD3, BRD4, c11orf95, CAMTA1, CCAR2, CCDC6, CCDC88A, CCDC170, CCNB3, CCND1, CD44, CD74, CEP85L, CIC, CLDN18, CLIP1, CLTC, CNTRL, COL1A1, CREB1, CREB3L1, CREB3L2, CRTC1, CTNNB1, DDIT3, DNAJB1, EGFR, EML4, EPC1, EPCAM, ERBB2, ERBB4, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, EZR, FEV, FGFR1, FGFR2, FGFR3, FLI1, FN1, FOXO1, FOXO4, FOXR2, FUS, GLI1, GOPC, GPR128, HEY1, HMGA2, HTRA1, IGF1R, INSR, JAK2, JAZF1, KIAA1549, KIF5B, KIT, LEUTX, LMNA, LPP, LTK, MAGI3, MAML1, MAML2, MAML3, MAMLD1, MAP3K8, MARS1, MAST1, MAST2, MEAF6, MET, MGA, MGMT, MITF, MKL2, MN1, MSH2, MYB, MYBL1, MYC, NAB2, NCOA1, NCOA2, NCOA3, NCOA4, NFATC2, NFIB, NOTCH2, NPM1, NR4A3, NRG1, NRG2, NSD3, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PAX7, PAX8, PBX1, PDGFB, PDGFD, PDGFRA, PDGFRB, PHF1, PIK3CA, PLAG1, PML, POU5F1, PPARG, PPARGC1A, PPP1CB, PRKACA, PRKAR1A, PRKCA, PRKCB, PRKD1, PRKD2, PRKD3, PTPRZ1, QKI, RAD51B, RAF1, RANBP2, RARA, RELA, RELCH, RET, ROS1, RPS6KB1, RREB1, RSPO2, RSPO3, SDC1, SDC4, SH3PXD2A,SLC1A2, SHTN1, SLC34A2, SLC44A1, SLC45A3, SND1, SQSTM1, SS18, SSX1, SSX2, SSX4, STAT6, STRN, SUZ12, TACC1, TACC2, TACC3, TAF2N, TAF15, TCF3, TCF12, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TPM3, TPR, TRIM24, TRIM33, TRIO, TTYH1, VGLL2, VGLL3, VMP1, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZMYM2, ZNF703<\/em><\/p>\n<\/div><\/div><\/div><\/i><\/i><\/span>List for specific transcript variants<\/span><\/a><\/h6><\/div>\nEGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
EGFR del ex2-22 (mLEEK), EGFR del ex25-26 (EGFRvIVb), EGFR del ex25-27 (EGFRvIVa), EGFR del ex26-27, EGFR del ex14-15 (vII), EGFR del ex2-7 (vIII), FGFR2IIIb, MET ex14 skipping, NFE2L2 ex2 skipping, PDGFRA del ex8-9<\/em><\/p>\n<\/div><\/div><\/div><\/div><\/div>Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
Additional output files are:<\/strong><\/p>\n\nfusions.tsv<\/span>\nA tabular listing of all detected fusions. This file is produced by STARfusion and is described in detail on the STARfusion wiki<\/a>. The most important columns are:\n<\/strong>(1) FusionName (The detected fusion, e.g. GNB4–ETV1) and\n(9) FFPM (The number of fragments per million supporting this fusion)<\/li>\nintragene_events.tsv<\/span>\nA tabular listing of all detected intra-gene (exon-skipping) events. This file has 6 columns:\n<\/strong>(1) Fusion Name, e.g. EGFR_VIII\n(2) HGNC symbol (gene name) of the affected gene\n(3)-(5) Genomic location of the skipping event, with respect to the hg19 reference genome\n(6) FFPM, the number of fragments per million supporting this event<\/li>\nall_reads.bam (+bai)<\/span>\nAn alignment of all sequenced reads to the hg19 reference genome<\/li>\nfusions_evidence_mapped.bam (+bai)<\/span>\nAlignments of only the reads supporting fusion events<\/li>\nfusion_evidence_details.html<\/span>\nA self-contained website with visualizations of the detected fusions<\/li>\n<\/ul>\nIntermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div><\/div><\/div><\/div>Disclaimer<\/h2><\/div>This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\nCeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>Downloads<\/h2><\/div>Application Note: A Smarter Way to Fish For Fusions<\/div>
Intermediate files for troubleshooting can be found in the subfolder intermediate\/. You can safely delete this folder if the analyses completes.<\/p>\n<\/div>
This software is provided as is, and for research use only. Not for use in diagnostic procedures.<\/p>\n
CeGaT GmbH makes no representations and extends no warranties of any kind, either express or implied, including warranties of merchantability, fitness for a particular purpose, non-infringement, design, output, throughput, and the absence of latent or other defects whether or not discoverable.<\/p>\n<\/div><\/div><\/div><\/div><\/div><\/div>