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Oshlack
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JAFFA
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions
https://github.com/Oshlack/JAFFA/wiki
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Inconsistency between jaffa_results.csv and intermediate files
#106
Puputnik
opened
1 month ago
0
Updated Dockerfile for easier deployment and consistent builds
#105
olliecheng
closed
1 month ago
1
mutated cells detection
#104
mms100
closed
1 month ago
10
Request for updated Jaffa resources
#103
AlexeyLarionovCranfield
opened
3 months ago
0
Bpipe error groovy.lang.MissingMethodException: No signature of method: bpipe.Branch.plus() is applicable for argument types: (String) values: [.fasta]
#102
wdesaintjean
closed
8 months ago
12
which exact GTF/GFF used for the JAFFA Reference Files?
#101
mdhitch
closed
7 months ago
3
terminate called after throwing an instance of 'std::out_of_range'
#100
mw18f
opened
10 months ago
1
how to pass qin=33 flag to bpipe command (JAFFAL)?
#99
agata-sm
closed
8 months ago
2
Custom references for JAFFAL !!!
#98
KMBelal
closed
4 months ago
1
BCOR:CCNB3 fusions not detected
#97
Dhwani-2410
closed
4 months ago
1
Support for T2T-CHM13?
#96
majdabdul
closed
8 months ago
1
BCL2 fusion not catched?
#95
asaki1986
closed
4 months ago
8
Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads
#94
RDorney
opened
1 year ago
8
Error on running ONT data
#93
parsboy66
opened
1 year ago
4
run with error
#92
asaki1986
closed
1 year ago
3
Java and Groovy error while first time using JAFFA version 2.3
#91
hkoseoglu
opened
1 year ago
3
stage report_3_gene_fusions failed
#90
sophielemoine
closed
4 months ago
3
arm64 mac
#89
itslittman
closed
1 year ago
3
Multiple threading is not working
#88
albuskilili
opened
1 year ago
12
Support for plant genomes
#87
Zhuxitong
closed
1 year ago
4
Permission denied error in "Stage filter_transcripts"
#86
yjx1217
closed
1 year ago
1
Installation issues
#85
skudashev
closed
2 years ago
0
Crash when no fusions are present
#84
nrhorner
opened
2 years ago
0
Incorrect number of spanning pairs
#83
nadiadavidson
closed
1 year ago
0
hg19_genCode19_blast.nhr
#82
km-2021
closed
1 year ago
1
Running JAFFA on osx-arm64
#81
nrhorner
closed
4 months ago
1
Errors when running multiple files JAFFAL
#80
EduardoGCCM
closed
2 years ago
3
"No fusions were found for the following samples: BT474-demo MCF7-demo"
#79
ReWeda
closed
4 months ago
7
--vanilla: command not found error
#78
jchang97
closed
2 years ago
3
Reads with incorrect qualities error
#77
evanwangx
closed
2 years ago
4
how to get Pig's known_fusions.txt file
#76
TianYHYA
closed
2 years ago
1
Error in filter_transcripts
#75
EduardoGCCM
closed
2 years ago
6
Please provide a conda wrapper for jaffal, as for other jaffa functionality
#74
oneillkza
opened
2 years ago
2
pacbio pre-processing
#73
gr8ape
closed
2 years ago
2
FASTA file not found when specifying outputName (JAFFA direct)
#72
Rmulet
opened
2 years ago
1
Trying to understand JAFFAL ONT intermediate file XXX_merged.fq.txt
#71
MikaQiao
closed
2 years ago
8
Fastq file names containing the string "sample" cause the pipeline to fail
#70
bioruffo
closed
2 years ago
3
jaffal error when using a non-supported genome
#69
Aurore-B
closed
2 years ago
3
Error when output directory specified
#68
shernadi
closed
2 years ago
2
Update compile_results.R
#67
MikeWLloyd
closed
2 years ago
1
zero size output
#66
aheravi
closed
2 years ago
1
resource usage to improve performance
#65
anoronh4
closed
2 years ago
6
request to point to reference directory outside of install directory
#64
anoronh4
closed
3 years ago
5
extract_seq_from_fasta not getting installed
#63
Troyee13
closed
3 years ago
3
A problem when run JAFFA
#62
xiaoguang-sjtu
closed
3 years ago
0
jaffal error
#61
readmanchiu
closed
3 years ago
2
failed for 1 sample only
#60
mei-du
closed
3 years ago
6
JAFFAL output
#59
Lux91
closed
3 years ago
2
error at stage filter_transcripts
#58
mei-du
closed
3 years ago
10
Help with using bioconda version of jaffa
#57
Dwooi7417
closed
2 years ago
24
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