nanoporetech/remora issues and pull requests

#200 - Question about remora training

Issue - State: open - Opened by spoweekkk about 1 month ago - 4 comments

#199 - PolyA tail inquiry

Issue - State: open - Opened by simonecaniONT about 1 month ago - 2 comments

#198 - Error running remora infer

Issue - State: open - Opened by johannesnicolaus 3 months ago - 2 comments

#197 - ”ValueError: need at least one array to concatenate“ when using remora model train on test data

Issue - State: closed - Opened by spoweekkk 3 months ago - 8 comments

#196 - Using remora model train miss the error "double free or corruption (out) Aborted (核心已转储)"

Issue - State: closed - Opened by spoweekkk 3 months ago - 4 comments

#195 - Question on the randomer dataset for the RNA inosine_m6A model

Issue - State: closed - Opened by ChaseWLW 3 months ago - 1 comment

#194 - kmer model conversion

Issue - State: closed - Opened by guangzhaocs 4 months ago - 1 comment

#193 - Sensitivity on chunk-context parameter

Issue - State: open - Opened by saroudant 4 months ago - 2 comments

#192 - Normalization method

Issue - State: closed - Opened by yuxinPenny 4 months ago - 1 comment

#191 - data prep

Issue - State: closed - Opened by Jeff-Field 5 months ago - 3 comments

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

Issue - State: closed - Opened by iza-mcac 5 months ago - 3 comments

#189 - Not enough chunks

Issue - State: closed - Opened by TKsh6 6 months ago - 1 comment

#188 - DRS m6A modified bases

Issue - State: closed - Opened by JhinJhinJhin 6 months ago - 5 comments

#187 - How to do a Tombo resquiggle with Remora ?

Issue - State: closed - Opened by Toinax 7 months ago - 2 comments

#186 - Remora dataset prepare: shuffling

Issue - State: closed - Opened by hengjwj 7 months ago - 1 comment

#185 - Calling m6a on RNA002

Issue - State: closed - Opened by JSluo888 7 months ago - 1 comment

#184 - Remora Dataset Prepare Ends Prematurely

Issue - State: closed - Opened by andrewgalbraith21 8 months ago - 2 comments

#183 - How can I use the model trained by remora in Dorado?

Issue - State: closed - Opened by leighv318 8 months ago - 1 comment

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

Issue - State: closed - Opened by dolittle007 8 months ago - 2 comments

#181 - RemoraError: Not enough chunks

Issue - State: closed - Opened by adrienvillain 8 months ago - 2 comments

#180 - Can remora infer take a directory of pod5s?

Issue - State: closed - Opened by lkwhite 8 months ago - 5 comments

#179 - Resquiggle

Issue - State: closed - Opened by JSluo888 8 months ago - 3 comments

#178 - io_read.seq, ref_seq and signal orientation for revserse mapping

Issue - State: closed - Opened by yuxinPenny 8 months ago - 7 comments

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

Issue - State: closed - Opened by sparkcyf 9 months ago - 1 comment

#176 - Parser Errors Handling Optimizer or Scheduler Arugment

Issue - State: closed - Opened by andrewgalbraith21 9 months ago - 2 comments

#175 - Masking Signal Points Outside of Kmer Context

Issue - State: closed - Opened by andrewgalbraith21 9 months ago - 2 comments

#174 - Resquiggle

Issue - State: closed - Opened by MarioRinBarr 9 months ago - 4 comments

#173 - 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.

Issue - State: closed - Opened by akhilp24 9 months ago - 4 comments

#172 - Support for Standalone 5mC and/or 5mCG in dorado Basecalling Model Version 4.3.0

Issue - State: closed - Opened by wietingj 10 months ago - 2 comments

#171 - Remora model finetuning

Issue - State: closed - Opened by palakela 10 months ago - 9 comments

#170 - Workflow to extract chunks for a randomer dataset

Issue - State: closed - Opened by moa4020 10 months ago - 1 comment

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

Issue - State: closed - Opened by hiruna72 10 months ago - 1 comment

#168 - Regarding m6A modified basecalling

Issue - State: closed - Opened by PRIYANKA-22091995 10 months ago - 7 comments

#167 - Unknown error in resquiggle command

Issue - State: closed - Opened by CarolinaA09 10 months ago - 2 comments

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

Issue - State: closed - Opened by mem3nto0 11 months ago - 4 comments

#165 - 100% training accuracy - unable to navigate mistake

Issue - State: closed - Opened by moa4020 12 months ago - 1 comment

#164 - Urgent Help: Cannot Speed up Metric Extraction script

Issue - State: closed - Opened by alexturcoo 12 months ago - 7 comments

#163 - Urgent Help Required: Regarding Error for modified basecalling

Issue - State: closed - Opened by PRIYANKA-22091995 about 1 year ago - 1 comment

#162 - Possible to call 4mC, 5mC, and 6mA?

Issue - State: closed - Opened by Ge0rges about 1 year ago - 2 comments

#161 - Add RNA Models to Pretrained Folder

Issue - State: closed - Opened by VBHerrenC about 1 year ago - 5 comments

#160 - Missing MD Tag Despite Being Able to See MD Tag in BAM File

Issue - State: closed - Opened by VBHarrisN about 1 year ago - 4 comments

#159 - Can adapter trimming affect move table and model training?

Issue - State: closed - Opened by andrewgalbraith21 about 1 year ago - 2 comments

#158 - ```get_io_reads()``` fails with ```Move table discordant with signal``` on some reads

Issue - State: closed - Opened by drivenbyentropy about 1 year ago - 7 comments

#157 - RNA modifications

Issue - State: closed - Opened by VahidJavaran about 1 year ago - 2 comments

#156 - How do I acheive Re-squiggling with Remora

Issue - State: closed - Opened by alexturcoo about 1 year ago - 3 comments

#155 - How/where to get prediction probablilities to plot ROC/PR curves?

Issue - State: closed - Opened by hengjwj about 1 year ago - 2 comments

#154 - Is mapping necessary to train my model?

Issue - State: closed - Opened by moa4020 about 1 year ago - 3 comments

#153 - Merging multiple models

Issue - State: closed - Opened by jorisbalc about 1 year ago - 4 comments

#152 - Alternative model

Issue - State: closed - Opened by philipmories about 1 year ago - 1 comment

#151 - raw signal to reference sequence?

Issue - State: closed - Opened by zhongzhd about 1 year ago - 3 comments

#150 - remora dataset prepare not support r9.5 chemistry?

Issue - State: closed - Opened by xieyy46 about 1 year ago - 3 comments

#149 - Failed to use R9.4 kmer table

Issue - State: closed - Opened by Modernism-01 about 1 year ago - 4 comments

#148 - Question: How to change modification names in model after training?

Issue - State: closed - Opened by hengjwj about 1 year ago - 2 comments

#147 - the exact input length of remora model？

Issue - State: closed - Opened by xieyy46 about 1 year ago - 3 comments

#146 - Train my own data

Issue - State: closed - Opened by comtigo about 1 year ago - 3 comments

#145 - the exact meaning of different fields in remora dataset prepare output

Issue - State: closed - Opened by xieyy46 about 1 year ago - 3 comments

#144 - Why finetuning an existing model?

Issue - State: closed - Opened by touala about 1 year ago - 1 comment

#143 - dna_r10.4.1_e8.2_400bps Compatible with both 5KHz and 4KHz

Issue - State: closed - Opened by andrewgalbraith21 about 1 year ago - 1 comment

#142 - make_config not found

Issue - State: closed - Opened by yifengyuan about 1 year ago - 1 comment

#141 - What causes differences in meth_qual distributions between samples?

Issue - State: closed - Opened by billytcl about 1 year ago - 1 comment

#140 - remora 3.0: error when training on different canonical bases

Issue - State: closed - Opened by Mathias-Boulanger about 1 year ago - 9 comments

#139 - Can m6A model was added in release v3.0.0 detect DNA m6A signal?

Issue - State: closed - Opened by 1Wencai about 1 year ago - 1 comment

#138 - ```ValueError: negative dimensions are not allowed``` when calling ```set_refine_signal_mapping()```

Issue - State: closed - Opened by drivenbyentropy about 1 year ago - 3 comments

#137 - --basecall-anchor overrides --focus-reference-positions in dataset prepare

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 2 comments

#136 - Cannot run the test example

Issue - State: closed - Opened by acms-llnl over 1 year ago - 6 comments

#135 - RemoraError: Move table discordant with signal

Issue - State: closed - Opened by alexcritschristoph over 1 year ago - 6 comments

#134 - Support for read splitting for ```dorado``` basecalled datasets

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 6 comments

#133 - Inaccurate calls in the modified sample and model training

Issue - State: closed - Opened by jorisbalc over 1 year ago

#132 - how to distinguish 5mC and 5hmC

Issue - State: closed - Opened by luming-zou over 1 year ago - 2 comments

#131 - Modified basecalling for supplementary alignments

Issue - State: closed - Opened by e-sollier over 1 year ago - 4 comments

#130 - documentation

Issue - State: closed - Opened by Jeff-Field over 1 year ago - 8 comments

#129 - Using pre-trained models for feature extraction

Issue - State: closed - Opened by parham-k over 1 year ago - 3 comments

#128 - Can Models Be Generalizable Across Sampling Rate

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 2 comments

#127 - training your own model

Issue - State: closed - Opened by AlineMuyle over 1 year ago - 5 comments

#126 - export older remora model as dorado format

Issue - State: closed - Opened by Yijun-Tian over 1 year ago - 4 comments

#125 - Non SAM mod base abbreviation support?

Issue - State: closed - Opened by jorisbalc over 1 year ago - 2 comments

#124 - Base modification detection for direct RNA sequencing

Issue - State: closed - Opened by keenhl over 1 year ago - 5 comments

#123 - Error while installing remora

Issue - State: closed - Opened by keenhl over 1 year ago - 9 comments

#122 - The difference between signal value “trimmean” and “dwell"

Issue - State: closed - Opened by Taojianchang over 1 year ago - 1 comment

#121 - Alternative mapper to produce input bam for e.g. model training

Issue - State: closed - Opened by schriwag over 1 year ago - 2 comments

#120 - Add query to ref coord mapping

Pull Request - State: open - Opened by chilampoon over 1 year ago - 2 comments

#119 - Problem with --num-duplex-prep-workers option in duplex_from_pod5_and_bam

Issue - State: closed - Opened by santanaw over 1 year ago - 3 comments

#118 - ref to signal mapping did not consider splicing

Issue - State: closed - Opened by chilampoon over 1 year ago - 6 comments

#117 - Error while installing remora

Issue - State: closed - Opened by Daniboy-boy over 1 year ago - 1 comment

#116 - Details regarding ```format_mm_ml_tags()```

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 2 comments

#115 - Remora infer on bed specified regions

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 2 comments

#114 - Clarification on the interplay between ```reverse_signal``` and ```ref_anchored```

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 2 comments

#113 - canonical sample vs modified sample

Issue - State: closed - Opened by BioRB over 1 year ago - 2 comments

#112 - Chunk Context Signal Points

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 6 comments

#111 - Understanding the output of ```sig_map_refiner.extract_levels()```

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 2 comments

#110 - Strategy advice on modified base detection approach using the remora API

Issue - State: closed - Opened by drivenbyentropy over 1 year ago - 14 comments

GitHub / nanoporetech/remora issues and pull requests