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dpryan79
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MethylDackel
A (mostly) universal methylation extractor for BS-seq experiments.
MIT License
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Confused by --nOT and --nOB and the examples provided in the issues section
#163
Flope
opened
3 weeks ago
2
Does MethylDackel support BSBolt alignment format?
#162
cemselb
opened
2 months ago
1
[help] Can I use MethylDackel for diploid reference genome please?
#161
lizhe-gis
opened
2 months ago
1
add all context to perread
#160
Javkhaa
closed
5 months ago
0
Can MethylDackel extract per-base methylation metrics for TAPS?
#159
SEvisual
opened
5 months ago
0
Alignment trimming for Soft Clip reads?
#158
iiiir
opened
6 months ago
0
Different CpG calls when using different regions of inclusion for Methyldackel extract
#157
MoniDR
opened
7 months ago
0
Devel
#156
abcoxyzide
closed
9 months ago
0
adds a feature to limit by insert size
#155
bwlang
opened
9 months ago
0
Question about minimum coverage
#154
desmodus1984
opened
10 months ago
0
Issue running MethylDackel extract in parallel mode using minConversionEfficiency
#152
blue-moon22
opened
12 months ago
0
Confused regarding CTOT, CTOB. Are there suggested values?
#151
Flope
closed
12 months ago
3
How to index genome file for MethylDackel?
#150
harshraj1919
opened
1 year ago
1
Mixed up reads within bam file
#149
jsikora93
opened
1 year ago
0
Could not repeat a CpG extraction with the same reference file and its index
#148
sttongjai
opened
1 year ago
2
about M-bias
#147
feihongloveworld
closed
1 year ago
1
Positions in cytosine_report did not match the regions in providing bed file
#146
huichanghuang
opened
1 year ago
0
Does indel effect the methylation calling or C context determination
#145
huichanghuang
opened
1 year ago
1
Fix end trimming off-by-one that caused overflow into qual and seq
#144
limwz01
closed
1 year ago
2
Fix wrong mapping position used for overlap computation
#143
limwz01
closed
1 year ago
1
mbias
#142
jsikora93
opened
1 year ago
1
Coverage of C sites
#141
jsikora93
closed
1 year ago
1
Clarification on definition of "unmethylated C"
#140
cvenney
closed
1 year ago
1
Installation failure: "bigWig.h: No such file or directory"
#139
phongphak
opened
2 years ago
1
CURL_OPENSSL conflict with samtools
#138
shraddhapai
opened
2 years ago
3
mbias result is different between bismark and bwameth output
#137
nnlrl
closed
2 years ago
1
per-fragment methylation
#136
BeyondTheProof
opened
2 years ago
2
Genome browsing from MethylDackel bedGraphCpG file
#135
emiliomastriani
opened
2 years ago
0
Understanding --minConversionEfficiency argument
#134
TSolDour
closed
2 years ago
1
Stand output
#133
simonbrd
opened
2 years ago
1
Chromosomes effected by methylation
#132
emiliomastriani
closed
2 years ago
4
Methylation profile for large genome organisms
#131
awieeeee
opened
2 years ago
5
do not recompile on "make test" and "make install"
#130
zemu-unile
closed
2 years ago
0
perRead output - print Bismark methylation call string?
#129
embertucci
opened
3 years ago
3
why cytosine_report output blank file?
#128
realzhang
opened
3 years ago
0
Strand specific extraction
#127
Tschichen
closed
3 years ago
2
Corrects invalid link
#126
bwlang
closed
3 years ago
0
implement #122, the --ignoreNH option
#125
dpryan79
closed
3 years ago
1
adds mappability to readme
#124
bwlang
closed
3 years ago
0
maxVariantFrac
#123
Dingersrun
opened
3 years ago
3
Min mapq option seems to be ignored / -q setting has no effect
#122
DaGaMs
closed
3 years ago
8
cytosine report and minConversionEfficiency
#121
nchernia
closed
3 years ago
1
Fixed segfault with mappability filtering, minor fixes.
#120
Valiec
closed
3 years ago
2
Implement #61, allow filtering by non-CpG conversion efficiency. Also…
#119
dpryan79
closed
3 years ago
0
Fix #117, bump version to 0.5.3
#118
dpryan79
closed
3 years ago
1
perRead --requireFlags and --ignoreFlags not working properly
#117
abcoxyzide
closed
3 years ago
1
cytosine_report differences and question
#116
nchernia
opened
3 years ago
3
perRead Invalid option '?'
#115
nchernia
closed
3 years ago
3
the -p option about a overlapping read
#114
gill0110
closed
3 years ago
1
Reimplement pileup overlap detection
#113
dpryan79
closed
3 years ago
1
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