nanoporetech/modkit

Issues

• Filtering accuracy question

  #297 opened 2 months ago by Ge0rges
  2

• m6A methylation analysis and explanation of output files

  #276 opened 3 months ago by JhinJhinJhin
  8

• Request: additional output columns for extract

  #270 opened 3 months ago by OberonDixon
  3

• Modkit calling methylation on incompatible nucleotide

  #286 opened 3 months ago by Ge0rges
  16

• modkit extract full and modkit extract calls

  #296 opened 2 months ago by Flower9618
  1

• Using segmenting on differential methylation

  #295 opened 2 months ago by Raya-Faigenbaum-Romm
  1

• bedMethyl index missing in dmr multi with replicates

  #294 opened 2 months ago by Yang990-sys
  3

• m6A analysis

  #290 opened 2 months ago by Taylorain
  4

• modkit dmr pair of pileup bed file subset to 4mC

  #279 opened 3 months ago by SimonChen1997
  6

• Documentation ambiguity

  #293 opened 2 months ago by Ge0rges
  1

• result from "modkit pileup" command

  #288 opened 3 months ago by Flower9618
  5

• how is calculate valid_coverage ? Different results between total read or subsample reads

  #292 opened 2 months ago by DelphIONe
  1

• Install failed: fatal error: '-fuse-linker-plugin', but liblto_plugin.so not found

  #291 opened 3 months ago by liuyang2006
  1

• How does Modkit handle long-read methylation 3D genomic data

  #289 opened 3 months ago by biozzq
  1

• Comparing between methylation patterns of different samples

  #277 opened 3 months ago by Raya-Faigenbaum-Romm
  6

• modkit executable file not found in PATH [singularity install]

  #284 opened 3 months ago by sahuno
  2

• All strands are "+" in the output of `modkit extract full`

  #287 opened 3 months ago by weishwu
  3

• Inferring Hypermethylated and Hypomethylated Bases from ModKit DMR Pair Results

  #283 opened 3 months ago by Bhavesh-Tiwarekar
  1

• Indexing error in dmr multi

  #285 opened 3 months ago by Ge0rges
  4

• benchmark comparison of DMR detection tool

  #281 opened 3 months ago by charliechen912ilovbash
  2

• performing single-site analysis

  #282 opened 3 months ago by Lijingtangbo
  1

• Strange bias between percent_modified and valid_coverage from modkit pileup

  #262 opened 4 months ago by flofloflo-cell
  9

• Difference in total counts of each probability per modification in different pore chemistries

  #269 opened 4 months ago by eesiribloom
  8

• Understanding strand information

  #280 opened 3 months ago by Ge0rges
  2

• Validity of correlation between different RNA modification calls

  #278 opened 3 months ago by mbosm
  1

• Redundant motifs from `modkit motif search`

  #272 opened 3 months ago by galenptacek
  4

• uncertain strand direction in the pileup bed file

  #274 opened 3 months ago by SimonChen1997
  6

• IGV shows Coverage not methylation values from BedMethyl

  #275 opened 3 months ago by sahuno
  2

• modkit pileup Processed ~0 reads and skipped zero reads.

  #273 opened 3 months ago by bakeronit
  2

• filter-threshold vs mod-threshold

  #271 opened 3 months ago by bencarty2
  2

• m6A comparison with Modkit dmr. assertion `left == right` failed?

  #265 opened 3 months ago by HJosephLee
  12

• Normalized the DMR scores

  #261 opened 4 months ago by Congnguyenn
  4

• adjust-mods for skipped reads

  #268 opened 4 months ago by ekushele
  1

• Update modkit 0.4.0 iusse

  #263 opened 4 months ago by Macdot3
  11

• Interpreting data quality from sample-probs

  #266 opened 4 months ago by kylepalos
  2

• Version number in release files might be wrong

  #267 opened 4 months ago by ewearpel
  1

• Links to new docs are broken

  #264 opened 4 months ago by billytcl
  1

• modkit pileup and summary difference

  #259 opened 4 months ago by SimonChen1997
  2

• Merge bedmethyl file

  #260 opened 4 months ago by meydaria
  1

• Issue with interpreting pileup output

  #254 opened 4 months ago by sumudu-rangika
  3

• how to interpret 5mC and 5hmC call for same position in the genome

  #258 opened 4 months ago by dasn588
  1

• Trouble in modkit entropy

  #251 opened 4 months ago by DKS3713
  4

• Using a negative control sample to inform thresholds?

  #257 opened 4 months ago by hackkr
  1

• modkit pileup - modified based code = 17802

  #256 opened 4 months ago by reJELIN
  1

• Setting appropriate thresholds for calling m6A and pseU using modkit pileup - What to make of high Nfail numbers?

  #255 opened 4 months ago by DepledgeLab
  1

• reagrding modkit output

  #253 opened 4 months ago by dasn588
  1

• --call-mods not working on m6a

  #252 opened 4 months ago by faulk-lab
  3

• How does modkit extract handle indels on reads?

  #249 opened 5 months ago by Fu-Yilei
  4

• Why is the value of fraction modified greater than 1 in the bedMethyl file but not in bedgragh file?

  #250 opened 5 months ago by 1Wencai
  3

• Estimated threshold values

  #248 opened 5 months ago by lkerr34
  0