dpryan79/MethylDackel

Issues

• Confused by --nOT and --nOB and the examples provided in the issues section

  #163 opened 2 months ago by Flope
  2

• Does MethylDackel support BSBolt alignment format?

  #162 opened 3 months ago by cemselb
  1

• [help] Can I use MethylDackel for diploid reference genome please?

  #161 opened 3 months ago by lizhe-gis
  1

• Could not repeat a CpG extraction with the same reference file and its index

  #148 opened a year ago by sttongjai
  2

• Can MethylDackel extract per-base methylation metrics for TAPS?

  #159 opened 7 months ago by SEvisual
  0

• per-fragment methylation

  #136 opened 2 years ago by BeyondTheProof
  2

• Alignment trimming for Soft Clip reads?

  #158 opened 8 months ago by iiiir
  0

• Different CpG calls when using different regions of inclusion for Methyldackel extract

  #157 opened 9 months ago by MoniDR
  0

• Question about minimum coverage

  #154 opened a year ago by desmodus1984
  0

• How to index genome file for MethylDackel?

  #150 opened a year ago by harshraj1919
  1

• Issue running MethylDackel extract in parallel mode using minConversionEfficiency

  #152 opened a year ago by blue-moon22
  0

• Confused regarding CTOT, CTOB. Are there suggested values?

  #151 opened a year ago by Flope
  3

• Mixed up reads within bam file

  #149 opened a year ago by jsikora93
  0

• about M-bias

  #147 opened 2 years ago by feihongloveworld
  1

• Positions in cytosine_report did not match the regions in providing bed file

  #146 opened 2 years ago by huichanghuang
  0

• Does indel effect the methylation calling or C context determination

  #145 opened 2 years ago by huichanghuang
  1

• mbias

  #142 opened 2 years ago by jsikora93
  1

• Coverage of C sites

  #141 opened 2 years ago by jsikora93
  1

• Can MethylDackel run for pbat?

  #110 opened 4 years ago by ifishlin
  4

• mbias result is different between bismark and bwameth output

  #137 opened 2 years ago by nnlrl
  1

• Clarification on definition of "unmethylated C"

  #140 opened 2 years ago by cvenney
  1

• --OT and --OB suggestions by mbias produce "Invalid bounds string"

  #112 opened 4 years ago by DaGaMs
  7

• Installation failure: "bigWig.h: No such file or directory"

  #139 opened 2 years ago by phongphak
  1

• CURL_OPENSSL conflict with samtools

  #138 opened 2 years ago by shraddhapai
  3

• Genome browsing from MethylDackel bedGraphCpG file

  #135 opened 3 years ago by emiliomastriani
  0

• Understanding --minConversionEfficiency argument

  #134 opened 3 years ago by TSolDour
  1

• Stand output

  #133 opened 3 years ago by simonbrd
  1

• Chromosomes effected by methylation

  #132 opened 3 years ago by emiliomastriani
  4

• Methylation profile for large genome organisms

  #131 opened 3 years ago by awieeeee
  5

• perRead output - print Bismark methylation call string?

  #129 opened 3 years ago by embertucci
  3

• why cytosine_report output blank file?

  #128 opened 3 years ago by realzhang
  0

• Strand specific extraction

  #127 opened 3 years ago by Tschichen
  2

• maxVariantFrac

  #123 opened 3 years ago by Dingersrun
  3

• Min mapq option seems to be ignored / -q setting has no effect

  #122 opened 3 years ago by DaGaMs
  8

• cytosine report and minConversionEfficiency

  #121 opened 3 years ago by nchernia
  1

• cytosine_report differences and question

  #116 opened 4 years ago by nchernia
  3

• perRead Invalid option '?'

  #115 opened 3 years ago by nchernia
  3

• perRead --requireFlags and --ignoreFlags not working properly

  #117 opened 4 years ago by abcoxyzide
  1

• the -p option about a overlapping read

  #114 opened 4 years ago by gill0110
  1

• MethylDackel core dump Ubintu 18.04 (problem happend again in issue #95)

  #99 opened 4 years ago by tahuh
  30

• methyldackel for GCH context

  #109 opened 4 years ago by vivekbhr
  1

• Incorrect strand assignment for single-end, non-directional libraries from Bismark

  #107 opened 4 years ago by mattsoup
  2

• nOT, nOB argument for tagmentation-based WGBS

  #108 opened 4 years ago by ifishlin
  1

• Compilation error - linker error

  #106 opened 4 years ago by mpBioinf
  3

• Segmentation fault with extract command

  #105 opened 4 years ago by nilaycan
  1

• Counts reported for G positions

  #104 opened 4 years ago by dataMaster-Kris
  1

• methylDackel extract segmentation fault

  #103 opened 4 years ago by acontrerasg
  1

• How to exclude the first 10bp of each read, irrespective of orientation

  #102 opened 5 years ago by DaGaMs
  9

• "Invalid bounds string" with the example setting from the help

  #101 opened 5 years ago by DaGaMs
  6

• The extraction speed differs a lot between bams from different mapping software

  #100 opened 5 years ago by chenzixi07
  4