Ecosyste.ms: Issues

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GitHub / nanoporetech/dorado issues and pull requests

#1130 - How to check the modification model version

Issue - State: open - Opened by hungweichen0327 3 months ago - 2 comments

#1128 - Dorado cannot find GPU

Issue - State: closed - Opened by baozg 3 months ago - 7 comments
Labels: cluster

#1127 - Issue with --estimate-poly-a

Issue - State: closed - Opened by Suchi-alt 3 months ago - 6 comments
Labels: polyA

#1126 - Methylation calling v5.0.0_5mCG_5hmCG@v2 model output non-CpG results

Issue - State: closed - Opened by liuyang2006 3 months ago - 6 comments

#1124 - Dorado demux unexplained unclassified read

Issue - State: open - Opened by GeorgescuC 3 months ago - 4 comments
Labels: barcode

#1123 - 'XM' tag not found by grep. (call from pod5)

Issue - State: closed - Opened by ysuzuki1978 3 months ago - 1 comment
Labels: documentation, mods

#1122 - m5C and inosine base-calling models argument not found

Issue - State: closed - Opened by kamaloxfordpathology 3 months ago - 2 comments

#1121 - SUP Modification Basecalling Model Architecture

Issue - State: closed - Opened by harikaurel 3 months ago - 1 comment
Labels: question, mods, models

#1120 - modified basecalling analysis for m6a modification of RNA

Issue - State: closed - Opened by Seongmin-Jang-1165 3 months ago - 2 comments
Labels: question, mods, models

#1119 - Recommended max_barcode_penalty for a given barcode length

Issue - State: closed - Opened by lonsbio 3 months ago - 5 comments
Labels: question, barcode

#1117 - Question on CpG Island-Specific Methylation Analysis Using Dorado

Issue - State: closed - Opened by Taylorain 3 months ago - 2 comments

#1116 - Automated Model Selection for Fast5 File to FastQ File

Issue - State: closed - Opened by pinkfairy57 3 months ago - 1 comment
Labels: documentation, models

#1115 - Duplex from pre-basecalled BAM

Issue - State: closed - Opened by jmpolinski 3 months ago - 4 comments
Labels: documentation, duplex

#1114 - Log command output failed

Issue - State: closed - Opened by liuyang2006 3 months ago - 2 comments
Labels: question

#1113 - dorado basecaller: model [email protected] slower than [email protected]

Issue - State: closed - Opened by davidebolo1993 3 months ago - 3 comments
Labels: performance

#1112 - Dorado correct running very slowly when merging different runs

Issue - State: closed - Opened by SimonaSecomandi 3 months ago - 3 comments
Labels: read_correction

#1111 - Dorado Demultiplexing Inconsistency

Issue - State: closed - Opened by okverynice 3 months ago - 3 comments
Labels: documentation, barcode

#1110 - Quality score differences when running dorado on the Gridion vs on a linux server

Issue - State: open - Opened by abridgeland 3 months ago - 3 comments
Labels: models

#1109 - Why was 260 bps deprecated?

Issue - State: closed - Opened by hjarnek 3 months ago - 8 comments
Labels: question

#1108 - estimate polyA doesn't find tails well with custom primer

Issue - State: open - Opened by shaohuishi 3 months ago - 3 comments
Labels: polyA

#1106 - correct from-paf does a little chunk then stops

Issue - State: open - Opened by matthewhvandam 3 months ago - 1 comment
Labels: read_correction

#1105 - Request CpG methylation detection command

Issue - State: closed - Opened by liuyang2006 3 months ago - 2 comments
Labels: models

#1104 - Where to get `2021-05-17_dna_r9.4.1_minion_96_29d8704b` model

Issue - State: closed - Opened by Rohit-Satyam 3 months ago - 2 comments

#1103 - Dorado 'sup' RAM overflow on Windows, only with large pod5 files (weird bug)

Issue - State: open - Opened by GabeAl 3 months ago - 1 comment
Labels: bug

#1102 - alignment with "dorado basecaller" command

Issue - State: open - Opened by Flower9618 3 months ago - 2 comments
Labels: question, aligner

#1101 - Significant decrease in demux yield going from dorado-v0.5.1 to dorado v >= 0.7.3

Issue - State: closed - Opened by wshropshire 4 months ago - 3 comments
Labels: barcode

#1100 - The lowest GPU memory required for dorado correct？

Issue - State: open - Opened by hrluo93 4 months ago - 3 comments
Labels: read_correction

#1099 - dorado: "-o" is now ambiguous: refers to both output directory and "overlap"

Issue - State: closed - Opened by GabeAl 4 months ago - 1 comment
Labels: duplicate

#1098 - Dorado 0.8.2 crashes when calling methylation

Issue - State: closed - Opened by Kirk3gaard 4 months ago - 6 comments
Labels: bug, mods

#1097 - Can Dorado move the Adaptor designed by us with known sequence

Issue - State: closed - Opened by LongYuan0529 4 months ago - 3 comments
Labels: documentation, polyA

#1096 - No supported chemistry found for flowcell_code:'_UNKNOWN_FLOWCELL_'

Issue - State: closed - Opened by chengyangWang-cell 4 months ago - 2 comments
Labels: models

#1095 - Automatic model selection fails for R10.4

Issue - State: closed - Opened by mjlarsen 4 months ago - 1 comment
Labels: models

#1094 - Request to make run name in output files from dorado demux an option

Issue - State: open - Opened by wshropshire 4 months ago - 2 comments
Labels: enhancement

#1093 - Output File Location Issues - Not sure if it reported the results.

Issue - State: closed - Opened by JPN96 4 months ago - 2 comments
Labels: cluster

#1092 - demuxing with custom dual barcoding

Issue - State: closed - Opened by nr0cinu 4 months ago - 4 comments

#1091 - Job Getting Killed After Creating Basecall Pipeline

Issue - State: closed - Opened by pinkfairy57 4 months ago - 4 comments

#1090 - Poly(A) Sequence and Subsequent Analysis

Issue - State: closed - Opened by x1han 4 months ago - 1 comment

#1089 - How does dorado handle 3D data

Issue - State: open - Opened by happier21 4 months ago - 4 comments
Labels: question

#1088 - dorado correct outputting empty fasta file

Issue - State: closed - Opened by afaqb2w 4 months ago - 2 comments

#1085 - Dorado Correct Run Using Reads from R9 Flow Cell

Issue - State: closed - Opened by PhDWannaB1030 4 months ago - 2 comments
Labels: duplicate

#1084 - --max-reads on dorado duplex

Issue - State: open - Opened by lucacozzuto 4 months ago - 1 comment
Labels: enhancement

#1083 - Movetable Output for Read that Maps to Reverse Strand

Issue - State: closed - Opened by j-o-song 4 months ago - 3 comments

#1082 - Replacement for the removed -Y option in dorado v0.8.1

Issue - State: closed - Opened by RxLoutre 4 months ago - 2 comments

#1081 - Dorado Correct Not Finishing

Issue - State: open - Opened by jp-jong 4 months ago - 2 comments
Labels: bug, read_correction

#1080 - Epigenetic Analysis Pipeline Issue: "Failed to Get Modbase Info AUX Data Not Found

Issue - State: open - Opened by priyanagpal25 4 months ago - 2 comments
Labels: mods

#1079 - Question about dorado correct

Issue - State: closed - Opened by tbenavi1 4 months ago - 1 comment
Labels: question, read_correction

#1078 - Dorado RNA Model training data characteristics

Issue - State: closed - Opened by williamphu 4 months ago - 1 comment
Labels: question

#1077 - Where to find new run_id field added in front of dorado demux outputs

Issue - State: closed - Opened by RxLoutre 4 months ago - 10 comments

#1076 - Unable To Use Automatic Model Selection

Issue - State: closed - Opened by pinkfairy57 4 months ago - 4 comments
Labels: models

#1074 - Using dorado trim to remove primers from both the end

Issue - State: closed - Opened by ashokpatowary 4 months ago - 6 comments
Labels: question, trim

#1073 - Dorado customer barcode demultiplex

Issue - State: closed - Opened by GingingYJ 4 months ago - 1 comment
Labels: documentation, barcode

#1072 - Threshold for methylation detection

Issue - State: closed - Opened by Taylorain 4 months ago - 8 comments

#1071 - 4 types of errors after upgrading from v0.7.2 to v0.8.1

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

#1070 - dorado 0.8.1 crashes when calling modificaitons

Issue - State: closed - Opened by Kirk3gaard 4 months ago - 11 comments

#1067 - Dorado duplex reads' mean quality are lower than simplex reads

Issue - State: open - Opened by ErminZ 4 months ago - 3 comments

#1065 - Dorado and IBM Power 9 AC922

Issue - State: open - Opened by HeLi-80 4 months ago - 5 comments

#1058 - Request for Guidance on Using Minimap2 for All-vs-All Read Alignment in Dorado Correct

Issue - State: closed - Opened by sebeier 4 months ago - 7 comments
Labels: read_correction

#1056 - Question re. basecalling correction

Issue - State: closed - Opened by li-xuyang28 4 months ago - 1 comment
Labels: question, read_correction

#1051 - Demultiplex custom barcode

Issue - State: closed - Opened by Seongmin-Jang-1165 4 months ago - 3 comments

#1040 - Dorado v0.8 for modified base calling runs slow

Issue - State: closed - Opened by shogohlab 4 months ago - 8 comments
Labels: performance

#1038 - V8 seems to be much slower

Issue - State: closed - Opened by weishwu 4 months ago - 5 comments
Labels: performance

#1037 - dorado basecaller has duplicate command line flag -o

Issue - State: open - Opened by lucast122 4 months ago - 1 comment
Labels: bug

#1036 - Can dorado demux based on the presence/absence of an adapter sequence?

Issue - State: closed - Opened by billytcl 5 months ago - 1 comment

#1032 - Dorado correct for R9 data

Issue - State: closed - Opened by asan-emirsaleh 5 months ago - 6 comments
Labels: read_correction

#1006 - dorado basecalling of recovered pod5 files not working

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

#1004 - Dorado aligner not working on input directory

Issue - State: closed - Opened by ilivyatan 5 months ago - 2 comments
Labels: documentation

#953 - Dorado model downloads incomplete and 'std::runtime_error'

Issue - State: closed - Opened by achang44 7 months ago - 2 comments
Labels: documentation, models

#935 - Minor Documentation Fix: Parameter Names for Custom Barcodes

Issue - State: closed - Opened by enc-wmatern 7 months ago - 2 comments
Labels: documentation

#905 - Megabase reads in v5 models

Issue - State: closed - Opened by diego-rt 8 months ago - 4 comments

#898 - Dorado basecall identified barcode but not trimmed in demux

Issue - State: closed - Opened by alexyfyf 8 months ago - 6 comments
Labels: question, barcode, trim

#876 - Minor: Argument parsing with the --modified-bases parameter

Issue - State: closed - Opened by rfran010 8 months ago - 2 comments
Labels: bug, documentation

#872 - barcoding_summary.txt issue

Issue - State: open - Opened by SalvadorGJ 8 months ago - 8 comments

#855 - Dorado 0.7.0 duplex with modified bases: throws '[error] basic_string::substr: __pos' and may abort

Issue - State: closed - Opened by janpb 8 months ago - 24 comments
Labels: bug, duplex, mods

#851 - `dorado correct` discarding reads in repeats

Issue - State: open - Opened by diego-rt 8 months ago - 16 comments
Labels: read_correction

#805 - Read splitting of concatemers

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

#801 - basecalling with hac v4.2 vs v4.3 model

Issue - State: closed - Opened by eesiribloom 9 months ago - 3 comments
Labels: question

#768 - Dorado 0.5.3 - memory issues - BAM truncated?

Issue - State: closed - Opened by cfrias-cnag 10 months ago - 21 comments
Labels: duplex

#722 - Dorado Demultiplexing

Issue - State: closed - Opened by akholwad 10 months ago - 3 comments
Labels: enhancement, barcode

#677 - How does chimeric read splitting work and how to take advantage of additional adapters

Issue - State: open - Opened by pclavell 11 months ago - 7 comments
Labels: question

#637 - Memory alignment issue on linux arm64 GH200

Issue - State: open - Opened by mp15 12 months ago - 9 comments
Labels: bug

#603 - Duplicate reads after basecalling

Issue - State: closed - Opened by MostafaYA about 1 year ago - 8 comments

#542 - Empty sequence and qstring provided for read id xyz

Issue - State: closed - Opened by avilella about 1 year ago - 7 comments
Labels: bug

#541 - Cuda out of memory

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

#465 - basecaller dorado-0.4.2-linux-x64 progress bar freeze at 50%

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

#315 - 9.4.1 simplex errors with sup and hac models on M2

Issue - State: closed - Opened by dbernick over 1 year ago - 8 comments
Labels: bug

#174 - All Contexts 5mC Methylation calling updates?

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

#100 - polyA sequence are not called by dorado

Issue - State: closed - Opened by yul96 almost 2 years ago - 27 comments
Labels: enhancement