timbitz/Whippet.jl

Issues

• Error during quantification of FASTQ files

  #118 opened 3 years ago by dBenedek
  12

• Regarding ArgumentError: cannot create a mer with ambiguous nucleotides

  #144 opened 8 months ago by PRIYANKA-22091995
  1

• ERROR: expected package `WaveletMatrices [c0580c95]` to be registered when compiling

  #142 opened 10 months ago by noahpieta
  2

• ERROR: LoadError: BoundsError: attempt to access BioSequences.LongDNASeq at index [65269405:65269446]

  #141 opened a year ago by dschwoerer
  1

• ERROR: LoadError: Cannot encode 78 to BioSequences.DNAAlphabet{2}()

  #139 opened a year ago by mrb20045
  3

• ERROR: LoadError: SystemError: opening file "/home/emanuele/Whippet.jl/bin/../index/graph.jls": No such file or directory

  #134 opened 2 years ago by emanueleraggi
  4

• Missing dependencies for Julia

  #138 opened 2 years ago by astrophys
  5

• How whippet is listing alternative events?

  #137 opened 2 years ago by pierreg2
  2

• Issue with BioSequences

  #135 opened 2 years ago by zoescherzer0318
  3

• psi

  #136 opened 2 years ago by shregeno8
  0

• Issue with ArgParse

  #133 opened 2 years ago by zoescherzer0318
  3

• How to interpret complexity column in the .psi.gz output files?

  #130 opened 2 years ago by MorticiaGiulia
  1

• jnc read count

  #129 opened 2 years ago by BeatrizdeToledo
  2

• Any idea to generate VCF/VEP files from Whippet output files?

  #131 opened 2 years ago by ptnaimelmm
  1

• Fastq.gz files from different lanes

  #132 opened 2 years ago by shregeno8
  1

• whippet-quant.jl does not output integer gene level read counts

  #128 opened 3 years ago by MiqG
  2

• whippet-quant.jl error

  #104 opened 3 years ago by JamalEH
  2

• There's an additional column in the output files

  #88 opened 3 years ago by aleighbrown
  1

• Where is "graph.jls"?

  #127 opened 3 years ago by justinjisu
  2

• ERROR: LoadError: BoundsError: attempt to access 2-element Array{Whippet.SGAlignNode,1} at index

  #124 opened 3 years ago by amitfenn
  2

• Optimal value for --bam-min-reads parameter

  #126 opened 3 years ago by narges-s
  1

• segfault using whippet-quant.jl

  #125 opened 3 years ago by tsgouros
  4

• Probability for deltaPsi

  #122 opened 3 years ago by OlgaVT
  2

• what is forum for code questions?

  #121 opened 3 years ago by tsgouros
  4

• error index in Serializing splice graph index...

  #123 opened 3 years ago by BeatrizdeToledo
  0

• bam index file in .csi format

  #120 opened 3 years ago by akshaya-v
  2

• ERROR: LoadError: UndefVarError: BAM not defined

  #116 opened 3 years ago by Alex-Nesta
  1

• --biascorrect specific error: LoadError: BoundsError: attempt to access 32nt DNA Sequence:

  #114 opened 3 years ago by rfara
  4

• curseq is GTCTTGTTGTTGGGCTTG of type BioSequences.BioSequence{BioSequences.DNAAlphabet{2}}

  #110 opened 3 years ago by rfara
  2

• whippet-quant ERROR: LoadError: UndefVarError: shuffle not defined

  #111 opened 3 years ago by rfara
  1

• regex ismatch deprecated for occursin

  #112 opened 3 years ago by timbitz
  0

• support for fasta files or bam files as input in whippet-quant?

  #105 opened 4 years ago by wbvguo
  0

• Option for reverse strand-specific data in bin/whippet-index.jl

  #108 opened 4 years ago by areyesq89
  0

• how does whippet define exon skip events?

  #107 opened 4 years ago by mhjiang97
  4

• Generate "sam | bam" files from the quantification step

  #106 opened 4 years ago by JamalEH
  0

• Feature Request: Variable boundaries like SUPPA

  #99 opened 4 years ago by Alex-Nesta
  3

• Splice junctions strandedness

  #103 opened 4 years ago by PeterVenhuizen
  1

• Is it normal to have different number of events for different samples with same index.jls?

  #102 opened 4 years ago by josegarciamanteiga
  2

• Indexing error

  #90 opened 5 years ago by ju-mu
  1

• LoadError: InexactError() with single end

  #100 opened 4 years ago by LucoLab
  0

• Quantification after creating an index supplemented with bam files produces NAs in evens of interest

  #98 opened 4 years ago by sopenaml
  3

• Question regarding relative proportion of TE events human transcriptome

  #96 opened 4 years ago by JamalEH
  10

• MA-like plot

  #97 opened 4 years ago by JamalEH
  0

• can I use .tpm.gz files to perform gene/transcript differential expression analysis?

  #91 opened 5 years ago by JamalEH
  2

• Error quantifying psi with fq.gz

  #94 opened 5 years ago by jordi-vaquero
  3

• How to compare .psi.gz files from two groups (or more than two samples) with different amount of samples in each condition.

  #92 opened 5 years ago by itszhengan
  0

• Merging bams for including novel splice sites makes a really big bam :(

  #87 opened 5 years ago by aleighbrown
  11

• Info about upcoming removal of packages in the General registry

  #89 opened 5 years ago by KristofferC
  0

• Creating annotation files

  #86 opened 5 years ago by Peter-J-Freeman
  1

• Error on whippet-quant.jl

  #85 opened 5 years ago by jordi-vaquero
  1