nanoporetech/modkit issues and pull requests

#100 - `pileup` does not allow gzipped reference sequence

Issue - State: open - Opened by JoukjeKloosterman about 1 year ago - 1 comment
Labels: enhancement

#99 - Performance on large bam files

Issue - State: closed - Opened by mattloose about 1 year ago - 12 comments

#98 - version reporting

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

#97 - modkit extract "--include-bed" Error: improperly formatted BED line

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

#96 - modkit

Issue - State: closed - Opened by duhuipeng about 1 year ago

#95 - Question about mod_qual value in modkit extract

Issue - State: open - Opened by liliaevgeniou about 1 year ago - 2 comments
Labels: question

#94 - Does the threshold estimation take into account edge-filter?

Issue - State: closed - Opened by billytcl about 1 year ago - 1 comment
Labels: documentation, question

#93 - Question about `dmr` score

Issue - State: closed - Opened by Ge0rges about 1 year ago - 12 comments
Labels: question

#92 - modkit pileup filter-threshold results in different calls

Issue - State: open - Opened by mattloose about 1 year ago - 5 comments
Labels: question

#91 - Clearer `A` and `B` notation

Issue - State: open - Opened by Ge0rges about 1 year ago - 3 comments

#90 - `dmr multi` still looks for `--regions`

Issue - State: open - Opened by Ge0rges about 1 year ago - 8 comments

#89 - dmr multi - error: 2 values required for '--sample <SAMPLES> <SAMPLES>' but 1 was provided

Issue - State: closed - Opened by flokraft85 about 1 year ago - 5 comments
Labels: documentation

#88 - Feature request? Position-dependent thresholding

Issue - State: open - Opened by billytcl about 1 year ago - 4 comments

#87 - Is there an easy way to generate % methylation by read position?

Issue - State: open - Opened by billytcl about 1 year ago - 6 comments
Labels: question

#86 - killed while using --bedgraph

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

#85 - Output command line seen as error in Slurm

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

#84 - Question about afterwork using modkit result & indexing bedMethyl files for igv

Issue - State: open - Opened by hyunjokoo about 1 year ago - 1 comment
Labels: question

#83 - `dmr` with coverage threshold

Issue - State: closed - Opened by Ge0rges about 1 year ago - 7 comments
Labels: enhancement

#82 - Zero reads recognized in megalodon basecalled .bam file

Issue - State: closed - Opened by OberonDixon about 1 year ago - 3 comments
Labels: question

#81 - bam index problem

Issue - State: closed - Opened by hyunjokoo about 1 year ago - 7 comments
Labels: question

#80 - Probability threshold

Issue - State: open - Opened by NickNCL about 1 year ago - 3 comments
Labels: question

#79 - Adjust-mods unexpected behaviour.

Issue - State: closed - Opened by mattloose about 1 year ago - 6 comments
Labels: documentation

#78 - Nicer error when `--regions-bed` file not found

Issue - State: closed - Opened by Ge0rges about 1 year ago - 3 comments

#77 - Different number of line in the bedMethyl table among samples

Issue - State: open - Opened by HeleneMeMartin about 1 year ago - 1 comment
Labels: question

#76 - Implicit-canonical mode

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

#75 - Traditional is confusing.

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

#74 - `modkit dmr multi` has incorrect output, and fails to do pairwise comparison

Issue - State: closed - Opened by Ge0rges over 1 year ago - 23 comments

#73 - `modkit dmr -o` should either create the output folder it doesn't exist or be clearer

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

#72 - `modkit dmr` detect header in the regions BED

Issue - State: closed - Opened by Ge0rges over 1 year ago - 1 comment

#71 - `modkit dmr multi` parametres are confusing

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

#70 - Does pileup work with 6mA

Issue - State: closed - Opened by Ge0rges over 1 year ago - 1 comment

#69 - Issue with remora models/dorado

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

#68 - Settings for modified basecalls in all contexts?

Issue - State: closed - Opened by bayraktar1 over 1 year ago - 2 comments

#67 - How to get only CpG sites from modkit extract output

Issue - State: closed - Opened by weishwu over 1 year ago - 6 comments
Labels: enhancement

#66 - trimmed.bam required for modkit repair

Issue - State: closed - Opened by Flower9618 over 1 year ago - 2 comments

#65 - Documentation update: Installation via Bioconda

Pull Request - State: closed - Opened by MatthiasZepper over 1 year ago - 4 comments

#64 - Log skipping reads that claim do not have modbase info, but I can see they do in the input bam

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

#63 - Matching of mods in modkit extract output to modkit pileup-hemi output

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

#62 - Modkit Extract Query Kmer and Ref Kmer Size

Issue - State: closed - Opened by andrewgalbraith21 over 1 year ago - 4 comments

#61 - modkit dmr output

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

#60 - [dmr] Report how many bedMethyl records fail to parse.

Issue - State: closed - Opened by PanZiwei over 1 year ago - 5 comments
Labels: enhancement, good first issue

#59 - modkit mdr over entire sequence

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

#58 - modkit dmr pair with replicates

Issue - State: closed - Opened by Ge0rges over 1 year ago - 1 comment

#57 - pileup-hemi input

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

#56 - What is the best practice workflow after Dorado?

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

#55 - Output both bedmethyl and bedgraph?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 1 comment

#54 - modkit repair: fatal runtime error: stack overflow

Issue - State: closed - Opened by tramelliwe over 1 year ago - 7 comments

#53 - modkit skipping reads

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

#52 - Modkit and modbam2bed

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

#51 - Modkit with bams generated from fast5 and not pod5

Issue - State: closed - Opened by assafgrw over 1 year ago - 10 comments

#50 - How to use the mod_qual in the modkit extract output?

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

#49 - Difficulties to run modkit with the modbases tutorial

Issue - State: open - Opened by marceelrf over 1 year ago - 2 comments
Labels: question

#48 - Workflow suggestions for follow-up metagenome analysis?

Issue - State: closed - Opened by Ge0rges over 1 year ago - 4 comments

#47 - Error in --include-bed: "Improperly formatted BED line"

Issue - State: closed - Opened by makise58 over 1 year ago - 2 comments

#46 - Inconsistence between per-site result and per-read result

Issue - State: closed - Opened by PanZiwei over 1 year ago - 10 comments

#45 - Install issue: libz-sys fail

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

#44 - fatal runtime error: stack overflow

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

#43 - modkit pileup bed output file has space delimited columns 10-18 and tab delimited 1-9

Issue - State: open - Opened by nextgenusfs over 1 year ago - 20 comments

#42 - unexpected behaviour from multiple modikit commands

Issue - State: closed - Opened by owenwilkins over 1 year ago - 11 comments

#41 - output different context (CG, CHG, CHH) in separate files

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

#40 - General range of --edge-filter for kb level sequencing

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

#39 - binaries are not up-to-date

Issue - State: closed - Opened by jayaprakash087 over 1 year ago - 1 comment

#38 - ImplicitProbModified

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

#37 - Question about cytosine count discrepancy in modified basecalling process

Issue - State: closed - Opened by bayraktar1 over 1 year ago - 4 comments

#36 - Extract mods option --exclude-bed (-v)

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

#35 - panic: index out of bounds

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

#34 - feat: add `ref_mod_strand` to `extract` output

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

#33 - incomplete output using duplex and bed with modkit extract

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

#32 - Error! zero reads in bam index

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

#31 - pileup warning "double added base mod calls for base C..."

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

#30 - modkit and unmapped reads in bam file from guppy

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

#29 - Call-mods Error: thread 'main' panicked at 'called `Option::unwrap()` on a `None` value'

Issue - State: closed - Opened by OOM-Killer415 over 1 year ago - 6 comments
Labels: bug

#28 - `error: unexpected argument '--collapse' found` for modkit 0.1.8

Issue - State: closed - Opened by PanZiwei over 1 year ago - 1 comment
Labels: documentation

#27 - differnt CpG sites when using different threads parameter

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

#26 - Unable to install on Ubuntu 20 (Illegal instruction in VM)

Issue - State: open - Opened by jcolicchio-soundag over 1 year ago - 12 comments

#25 - [call-mods] `--no-filtering` broken, use `--filter-threshold 0.0` instead

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

#24 - offset in motif-bed

Issue - State: closed - Opened by Violeta-de-Anca over 1 year ago - 2 comments
Labels: question

#23 - modkit: command not found

Issue - State: closed - Opened by gsukrit over 1 year ago - 10 comments

#22 - About the output of modkit

Issue - State: closed - Opened by Flower9618 over 1 year ago - 5 comments
Labels: question

#21 - Empty bed file

Issue - State: closed - Opened by Violeta-de-Anca over 1 year ago - 5 comments
Labels: documentation

#20 - How does modkit handle secondary/supplementary alignments?

Issue - State: closed - Opened by billytcl over 1 year ago - 3 comments
Labels: question

#19 - Mixed delimiter types in output bed file

Issue - State: closed - Opened by billytcl over 1 year ago - 2 comments
Labels: question

#18 - [ERROR] double added base mod calls for base C and read X,potentially a logic error!

Issue - State: closed - Opened by billytcl over 1 year ago - 9 comments
Labels: logging

#17 - Per-read support?

Issue - State: closed - Opened by PanZiwei over 1 year ago - 8 comments
Labels: enhancement

#16 - Output bed for every CpG position

Issue - State: closed - Opened by billytcl over 1 year ago - 8 comments
Labels: question

#15 - Failed modification calls

Issue - State: closed - Opened by pwh124 over 1 year ago - 3 comments

#14 - Comparison between `modkit` and `modbam2bed`.

Issue - State: open - Opened by qiangfu-eu over 1 year ago - 31 comments

#13 - Setting dual thresholds with modkit

Issue - State: closed - Opened by pwh124 over 1 year ago - 8 comments

#12 - Possible option to constrain `summary` only to the aligned bases?

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

#11 - Log skipped and discarded reads, such as HardClip reads from minimap2

Issue - State: closed - Opened by qiangfu-eu over 1 year ago - 4 comments
Labels: enhancement, logging

#10 - Option '--filter-threshold' of `summary`

Issue - State: closed - Opened by qiangfu-eu over 1 year ago - 7 comments
Labels: bug

#9 - Segfault on the cliveome

Issue - State: open - Opened by mp15 over 1 year ago - 6 comments

#8 - Options of 'summary'

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

#7 - modkit settings for rerio flip-flop modified base models

Issue - State: closed - Opened by Yijun-Tian almost 2 years ago - 4 comments

#6 - Q: `--filter-threshold FRAC` description

Issue - State: closed - Opened by sklages almost 2 years ago - 2 comments

#5 - Q: compared to modbam2bed?

Issue - State: closed - Opened by sklages almost 2 years ago - 2 comments

GitHub / nanoporetech/modkit issues and pull requests