Oshlack/JAFFA

Issues

• "No fusions were found for the following samples: BT474-demo MCF7-demo"

  #79 opened 20 days ago by ReWeda
  7

• Error on running ONT data

  #93 opened a year ago by parsboy66
  2

• Custom references for JAFFAL !!!

  #98 opened 10 months ago by KMBelal
  1

• which exact GTF/GFF used for the JAFFA Reference Files?

  #101 opened 3 months ago by mdhitch
  3

• Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

  #94 opened a year ago by RDorney
  8

• Bpipe error groovy.lang.MissingMethodException: No signature of method: bpipe.Branch.plus() is applicable for argument types: (String) values: [.fasta]

  #102 opened 5 months ago by wdesaintjean
  9

• how to pass qin=33 flag to bpipe command (JAFFAL)?

  #99 opened 5 months ago by agata-sm
  2

• Support for T2T-CHM13?

  #96 opened 5 months ago by majdabdul
  1

• BCOR:CCNB3 fusions not detected

  #97 opened a year ago by Dhwani-2410
  1

• terminate called after throwing an instance of 'std::out_of_range'

  #100 opened 6 months ago by mw18f
  1

• Java and Groovy error while first time using JAFFA version 2.3

  #91 opened a year ago by hkoseoglu
  3

• BCL2 fusion not catched?

  #95 opened a year ago by asaki1986
  8

• run with error

  #92 opened a year ago by asaki1986
  3

• stage report_3_gene_fusions failed

  #90 opened a year ago by sophielemoine
  3

• arm64 mac

  #89 opened a year ago by itslittman
  3

• Multiple threading is not working

  #88 opened 2 years ago by albuskilili
  12

• Support for plant genomes

  #87 opened 2 years ago by Zhuxitong
  4

• hg19_genCode19_blast.nhr

  #82 opened 2 years ago by km-2021
  1

• Incorrect number of spanning pairs

  #83 opened 2 years ago by nadiadavidson
  0

• Permission denied error in "Stage filter_transcripts"

  #86 opened 2 years ago by yjx1217
  1

• Trying to understand JAFFAL ONT intermediate file XXX_merged.fq.txt

  #71 opened 2 years ago by MikaQiao
  8

• Installation issues

  #85 opened 2 years ago by skudashev
  0

• Please provide a conda wrapper for jaffal, as for other jaffa functionality

  #74 opened 2 years ago by oneillkza
  2

• Crash when no fusions are present

  #84 opened 2 years ago by nrhorner
  0

• Running JAFFA on osx-arm64

  #81 opened 2 years ago by nrhorner
  1

• Help with using bioconda version of jaffa

  #57 opened 2 years ago by Dwooi7417
  24

• Errors when running multiple files JAFFAL

  #80 opened 2 years ago by EduardoGCCM
  3

• hg19 reference files for JAFFA version 2

  #56 opened 2 years ago by nadiadavidson
  3

• Reads with incorrect qualities error

  #77 opened 2 years ago by evanwangx
  4

• zero size output

  #66 opened 2 years ago by aheravi
  1

• resource usage to improve performance

  #65 opened 2 years ago by anoronh4
  6

• pacbio pre-processing

  #73 opened 2 years ago by gr8ape
  2

• how to get Pig's known_fusions.txt file

  #76 opened 2 years ago by TianYHYA
  1

• Error in filter_transcripts

  #75 opened 2 years ago by EduardoGCCM
  6

• --vanilla: command not found error

  #78 opened 2 years ago by jchang97
  3

• Error when output directory specified

  #68 opened 2 years ago by shernadi
  2

• Fastq file names containing the string "sample" cause the pipeline to fail

  #70 opened 2 years ago by bioruffo
  3

• FASTA file not found when specifying outputName (JAFFA direct)

  #72 opened 2 years ago by Rmulet
  1

• jaffal error when using a non-supported genome

  #69 opened 2 years ago by Aurore-B
  3

• request to point to reference directory outside of install directory

  #64 opened 3 years ago by anoronh4
  5

• jaffal error

  #61 opened 3 years ago by readmanchiu
  2

• extract_seq_from_fasta not getting installed

  #63 opened 3 years ago by Troyee13
  3

• A problem when run JAFFA

  #62 opened 3 years ago by xiaoguang-sjtu
  0

• failed for 1 sample only

  #60 opened 3 years ago by mei-du
  6

• JAFFAL output

  #59 opened 3 years ago by Lux91
  2

• error at stage filter_transcripts

  #58 opened 3 years ago by mei-du
  10

• The reference file version problem

  #55 opened 3 years ago by GAOwy123
  2

• True 120 Fusions MiSeq Dataset

  #49 opened 4 years ago by Evansef
  2

• Problems with running the pipeline completly

  #51 opened 4 years ago by chalkidiki
  18

• Failing at stage run_check

  #50 opened 4 years ago by SamHill95
  7