nanoporetech/remora

Issues

• Sensitivity on chunk-context parameter

  #193 opened 19 days ago by saroudant
  0

• Normalization method

  #192 opened 20 days ago by yuxinPenny
  0

• data prep

  #191 opened 22 days ago by Jeff-Field
  3

• IndexError: list index out of range when running remora dataset prepare due to k-mer table parsing

  #190 opened a month ago by iza-mcac
  3

• Not enough chunks

  #189 opened 2 months ago by TKsh6
  1

• Parser Errors Handling Optimizer or Scheduler Arugment

  #176 opened 3 months ago by andrewgalbraith21
  2

• Remora model finetuning

  #171 opened 3 months ago by palakela
  9

• DRS m6A modified bases

  #188 opened 3 months ago by JhinJhinJhin
  5

• How to do a Tombo resquiggle with Remora ?

  #187 opened 3 months ago by Toinax
  2

• io_read.seq, ref_seq and signal orientation for revserse mapping

  #178 opened 3 months ago by yuxinPenny
  7

• the exact meaning of different fields in remora dataset prepare output

  #145 opened 3 months ago by xieyy46
  3

• Alternative model

  #152 opened 3 months ago by philipmories
  1

• Regarding m6A modified basecalling

  #168 opened 3 months ago by PRIYANKA-22091995
  7

• Remora dataset prepare: shuffling

  #186 opened 3 months ago by hengjwj
  1

• Resquiggle

  #174 opened 5 months ago by MarioRinBarr
  4

• Calling m6a on RNA002

  #185 opened 3 months ago by JSluo888
  1

• Question about data preparation for training “All Context” modification model on Remora and the questions about the --refine-kmer-level-table input

  #177 opened 3 months ago by sparkcyf
  1

• Resquiggle

  #179 opened 3 months ago by JSluo888
  3

• Can Remora generate visualizations of the raw signal in a manner similar to the signal-to-reference mode of squigualiser?

  #182 opened 3 months ago by dolittle007
  2

• Remora Dataset Prepare Ends Prematurely

  #184 opened 4 months ago by andrewgalbraith21
  2

• RemoraError: Not enough chunks

  #181 opened 4 months ago by adrienvillain
  2

• How can I use the model trained by remora in Dorado?

  #183 opened 4 months ago by leighv318
  1

• Can remora infer take a directory of pod5s?

  #180 opened 4 months ago by lkwhite
  5

• Possible to call 4mC, 5mC, and 6mA?

  #162 opened 8 months ago by Ge0rges
  2

• Add RNA Models to Pretrained Folder

  #161 opened 5 months ago by VBHerrenC
  5

• Masking Signal Points Outside of Kmer Context

  #175 opened 5 months ago by andrewgalbraith21
  2

• Remora Model Training with Apple Silicon (M3 Pro) -> TypeError: Cannot convert a MPS Tensor to float64 dtype as the MPS framework doesn't support float64. Please use float32 instead.

  #173 opened 5 months ago by akhilp24
  2

• ```get_io_reads()``` fails with ```Move table discordant with signal``` on some reads

  #158 opened 6 months ago by drivenbyentropy
  7

• Workflow to extract chunks for a randomer dataset

  #170 opened 6 months ago by moa4020
  1

• 100% training accuracy - unable to navigate mistake

  #165 opened 6 months ago by moa4020
  1

• Urgent Help: Cannot Speed up Metric Extraction script

  #164 opened 6 months ago by alexturcoo
  7

• Remora re-squiggle (refine_signal_map.SigMapRefiner) on RNA data

  #166 opened 6 months ago by mem3nto0
  4

• Unknown error in resquiggle command

  #167 opened 6 months ago by CarolinaA09
  2

• Support for Standalone 5mC and/or 5mCG in dorado Basecalling Model Version 4.3.0

  #172 opened 6 months ago by wietingj
  2

• writing the signal alignment to an output file in SAM format using auxiliary tag 'ss'

  #169 opened 6 months ago by hiruna72
  1

• Merging multiple models

  #153 opened 8 months ago by jorisbalc
  4

• Question: How to change modification names in model after training?

  #148 opened 8 months ago by hengjwj
  2

• Train my own data

  #146 opened 8 months ago by comtigo
  3

• the exact input length of remora model？

  #147 opened 8 months ago by xieyy46
  3

• Why finetuning an existing model?

  #144 opened 8 months ago by touala
  1

• remora dataset prepare not support r9.5 chemistry?

  #150 opened 8 months ago by xieyy46
  3

• RNA modifications

  #157 opened 8 months ago by VahidJavaran
  2

• Is mapping necessary to train my model?

  #154 opened 8 months ago by moa4020
  3

• Urgent Help Required: Regarding Error for modified basecalling

  #163 opened 8 months ago by PRIYANKA-22091995
  1

• Missing MD Tag Despite Being Able to See MD Tag in BAM File

  #160 opened 9 months ago by VBHarrisN
  4

• How do I acheive Re-squiggling with Remora

  #156 opened 9 months ago by alexturcoo
  3

• Can adapter trimming affect move table and model training?

  #159 opened 9 months ago by andrewgalbraith21
  2

• How/where to get prediction probablilities to plot ROC/PR curves?

  #155 opened 10 months ago by hengjwj
  2

• raw signal to reference sequence?

  #151 opened 10 months ago by zhongzhd
  3

• Failed to use R9.4 kmer table

  #149 opened 10 months ago by Modernism-01
  4