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suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
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Error while running draw_fusion.R #234

Open Rezwanuzzaman opened 3 months ago

Rezwanuzzaman commented 3 months ago

Loading annotation Read 3010595 records Loading protein domains Read 134356 records Drawing fusion #1: AGAP3:BRAF Error in text.default(tip, y + 0.03, bandName, cex = fontSize, adj = c(0.5, : zero-length 'labels' specified Calls: drawIdeogram -> text -> text.default Execution halted

suhrig commented 3 months ago

Can you send me the content of the file you passed as an argument to --cytobandsFile as well as the first fusion of the fusions file?

Which version of Arriba is this?

Rezwanuzzaman commented 3 months ago

@suhrig I use Arriba 2.4.0. --fusions=fusions.tsv --cytobands=database/cytobands_hg19_hs37d5_GRCh37_v2.4.0.tsv

suhrig commented 3 months ago

Can you send me the first fusion of the fusions file (AGAP3:BRAF)?

Rezwanuzzaman commented 3 months ago

gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers

AGAP3 BRAF +/+ -/- 7:151128684 7:140787584 CDS/splice-site CDS/splice-site inversion 7 11 1 378 486 high in-frame . PH_domain(28%),Ras_family(100%)|Protein_kinase_domain(100%) . . ENSG00000133612 ENSG00000157764 ENST00000463381 ENST00000496384 downstream downstream duplicates(82) CGGGAGAAGAAGGCTGCCGAGTGCAAGGTGGACAGCATCGGGAGCGGCCGCGCCATCCCCATCAAGCAGGGGATCCTGCTAAAGCGGAGCGGCAAGTCCCTGAACAAGGAGTGGAAGAAGAAGTATGTGACGCTCTGTGACAACGGGCTGCTCACCTATCACCCCAGCCTGCAT|GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCTACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCAGGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATG___AAAACACTTGGTAGACGGGACTCGAGTGATGATTGGGA REKKAAECKVDSIGSGRAIPIKQGILLKRSGKSLNKEWKKKYVTLCDNGLLTYHPSLH|DLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKSSSSSEDRNRMKTLGRRDSSDDW K00102:513:HHM7KBBXY:7:1109:15158:33949,K00102:513:HHM7KBBXY:7:1115:18588:40174,K00102:517:HJTWNBBXY:1:1101:5690:7416,K00102:517:HJTWNBBXY:1:1110:29203:1490,K00102:517:HJTWNBBXY:1:1118:2909:4040,K00102:517:HJTWNBBXY:1:1122:16204:2246,K00102:517:HJTWNBBXY:1:1122:2605:31962,K00102:517:HJTWNBBXY:1:1208:23551:47999,K00102:517:HJTWNBBXY:1:1223:6066:44394,K00102:517:HJTWNBBXY:1:2114:11292:22186,K00102:517:HJTWNBBXY:2:2107:8714:30978,K00102:517:HJTWNBBXY:2:2122:15818:6361,K00102:517:HJTWNBBXY:3:1124:27702:12708,K00102:517:HJTWNBBXY:3:1227:11231:7169,K00102:517:HJTWNBBXY:3:2216:14468:44640,K00102:517:HJTWNBBXY:4:1105:12225:13253,K00102:517:HJTWNBBXY:4:1125:2067:36939,K00102:517:HJTWNBBXY:4:1126:11221:38803,K00102:517:HJTWNBBXY:4:1126:12418:2439,K00102:517:HJTWNBBXY:4:1204:5132:10598,K00102:517:HJTWNBBXY:4:1212:2199:8752,K00102:517:HJTWNBBXY:4:1212:29802:41809,K00102:517:HJTWNBBXY:4:2124:22374:48597,K00102:517:HJTWNBBXY:5:2201:27499:37114,K00102:517:HJTWNBBXY:5:2213:14905:7486,K00102:517:HJTWNBBXY:5:2218:31649:13042,K00102:517:HJTWNBBXY:5:2220:7517:38222,K00102:517:HJTWNBBXY:6:1104:9759:7750,K00102:517:HJTWNBBXY:6:1111:25033:10897,K00102:517:HJTWNBBXY:6:2203:24667:7451,K00102:517:HJTWNBBXY:6:2215:31274:16436,K00102:517:HJTWNBBXY:7:2202:16173:14713,K00102:523:HK7FLBBXY:1:2116:14478:13886,K00102:523:HK7FLBBXY:1:2116:15229:13113,K00102:523:HK7FLBBXY:1:2224:10013:47014,K00102:523:HK7FLBBXY:1:2228:10125:16084,K00102:523:HK7FLBBXY:2:1113:17614:13939,K00102:523:HK7FLBBXY:2:2207:30655:10510,K00102:523:HK7FLBBXY:2:2225:12936:29641,K00102:523:HK7FLBBXY:3:1227:22414:3793,K00102:523:HK7FLBBXY:4:1207:26423:10669,K00102:523:HK7FLBBXY:4:1228:21887:40965,K00102:523:HK7FLBBXY:4:2115:10906:8928,K00102:523:HK7FLBBXY:4:2214:9851:45010,K00102:523:HK7FLBBXY:4:2227:16001:10862,K00371:401:HFH3NBBXY:3:2104:26666:22379,K00371:401:HFH3NBBXY:4:1214:10439:38046,K00371:401:HFH3NBBXY:4:1214:16244:11987,K00371:401:HFH3NBBXY:4:2110:12266:44060,K00371:401:HFH3NBBXY:4:2208:9810:43708,K00371:401:HFH3NBBXY:5:1125:12794:4004,K00371:401:HFH3NBBXY:5:1212:30228:41528,K00371:401:HFH3NBBXY:5:2122:23155:21571,K00371:401:HFH3NBBXY:5:2221:25986:11671,K00371:401:HFH3NBBXY:6:1126:28909:32279,K00371:401:HFH3NBBXY:6:1201:2676:42038,K00371:401:HFH3NBBXY:6:1203:20791:13570,K00371:401:HFH3NBBXY:6:1206:4553:35620,K00371:401:HFH3NBBXY:7:2102:9222:2949,K00371:401:HFH3NBBXY:7:2110:14093:5165,K00371:401:HFH3NBBXY:8:2124:11008:23628,K00102:513:HHM7KBBXY:7:1104:23033:11126,K00102:513:HHM7KBBXY:7:1203:31050:42108,K00102:513:HHM7KBBXY:7:1214:8917:9631,K00102:513:HHM7KBBXY:7:1222:27225:13957,K00102:517:HJTWNBBXY:1:1101:31527:31154,K00102:517:HJTWNBBXY:2:1215:24190:27232,K00102:517:HJTWNBBXY:2:1223:3397:34002,K00102:517:HJTWNBBXY:2:1223:4219:32859,K00102:517:HJTWNBBXY:2:2117:5000:36218,K00102:517:HJTWNBBXY:3:2112:15737:32279,K00102:517:HJTWNBBXY:3:2210:6471:9789,K00102:517:HJTWNBBXY:4:2107:3427:45942,K00102:517:HJTWNBBXY:4:2208:31253:48438,K00102:517:HJTWNBBXY:5:1203:17452:18616,K00102:517:HJTWNBBXY:8:1127:3792:36059,K00102:517:HJTWNBBXY:8:1222:10206:9578,K00102:517:HJTWNBBXY:8:2208:22364:41053,K00102:517:HJTWNBBXY:8:2216:31010:36552,K00102:523:HK7FLBBXY:1:1215:17543:1930,K00102:523:HK7FLBBXY:1:1218:23926:39436,K00102:523:HK7FLBBXY:1:1228:31071:28991,K00102:523:HK7FLBBXY:2:1114:14864:46205,K00102:523:HK7FLBBXY:2:1114:14976:46012,K00102:523:HK7FLBBXY:2:2220:16244:42407,K00102:523:HK7FLBBXY:3:2206:2869:24085,K00371:401:HFH3NBBXY:4:2111:25378:43919,K00371:401:HFH3NBBXY:4:2121:9303:31962,K00371:401:HFH3NBBXY:5:2101:2747:7767,K00371:401:HFH3NBBXY:6:1207:3062:3952,K00371:401:HFH3NBBXY:6:2218:27123:40297,K00371:401:HFH3NBBXY:7:2119:16062:42618,K00371:401:HFH3NBBXY:8:1108:11160:17632,K00371:401:HFH3NBBXY:8:2217:11180:12779,K00102:513:HHM7KBBXY:7:2219:26880:41880,K00102:517:HJTWNBBXY:3:1113:11464:30890,K00102:517:HJTWNBBXY:3:1113:11495:30732,K00102:517:HJTWNBBXY:5:2118:20841:47313,K00102:523:HK7FLBBXY:2:2210:23104:24823,K00371:401:HFH3NBBXY:8:1214:22749:25720,K00371:401:HFH3NBBXY:8:2224:5923:12954

suhrig commented 3 months ago

I cannot reproduce the error. Which GTF file did you use to run Arriba and which one did you use to run draw_fusions.R?

Rezwanuzzaman commented 3 months ago

Please look --

./draw_fusions.R \ --fusions=...../sample.arriba.fusions.tsv \ --alignments=..../sample.sortedByCoord.out.bam \ --output=sample.fusions.pdf \ --annotation=.../rnafusion_3.0.0/REFERENCES/ensembl/Homo_sapiens.GRCh38.102.gtf \ --cytobands=..../rnafusion_3.0.0/REFERENCES/arriba/cytobands_mm10_GRCm38_v2.4.0.tsv \ --proteinDomains=.../rnafusion_3.0.0/REFERENCES/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3

suhrig commented 3 months ago

In the beginning you wrote that you used cytobands_hg19_hs37d5_GRCh37_v2.4.0.tsv for the cytobands file. Now you write that you used cytobands_mm10_GRCm38_v2.4.0.tsv. What did you actually do? Regardless, both are wrong. The fusions file is based on hg38/GRCh38. All the input files of draw_fusions.R should have GRCh38 in the name. I have no problems running the script with the correct input files and your fusions file.

suhrig commented 2 months ago

Do you need any further help on this?