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Issues list

Thank you, for the amazing tool, I have 9 bedmethyl files(4 control and 5 disease cases), these files generated from modkit tool. I have some questions question Looking for clarification on inputs and/or outputs
#328 opened Jan 2, 2025 by ralanany
1
Clarification on Modkit DMR Pair Results and Validate Accuracy question Looking for clarification on inputs and/or outputs
#327 opened Dec 31, 2024 by BrendanBeahan
4
Out of memory in modkit find-motifs troubleshooting workflow and data preparation questions
#323 opened Dec 27, 2024 by hannan666666
4
EOY release and thank you good first issue Good for newcomers
#320 opened Dec 21, 2024 by ArtRand
Failed to read fasta index (error 2) troubleshooting workflow and data preparation questions
#319 opened Dec 20, 2024 by ramnageena11
5
Compare methylation at a position between different genotype groups
#318 opened Dec 15, 2024 by sumudu-rangika
4
How to annotate bedmethyl file with cpg name instead of chr name and position and How can I find the pvalue for association of the cpg with the phenotype? question Looking for clarification on inputs and/or outputs
#317 opened Dec 15, 2024 by ralanany
4
modkit DMR result not as expected question Looking for clarification on inputs and/or outputs
#316 opened Dec 13, 2024 by baibhav-bioinfo
3
Error (0658) troubleshooting workflow and data preparation questions
#315 opened Dec 11, 2024 by ramnageena11
2
Sorting of extract calls output and tabix indexing question Looking for clarification on inputs and/or outputs
#313 opened Dec 10, 2024 by richardheery
1
How to get gzipped tab-separated-values (tabix file) from bedmethyl file generated by modkit, for down stream analysis by nanomethviz R package? question Looking for clarification on inputs and/or outputs
#312 opened Dec 10, 2024 by ralanany
6
Get haplotag info in modkit extract enhancement New feature or request
#310 opened Dec 6, 2024 by rowanhowellGE
1
fetching sequence failed error message when running pileup question Looking for clarification on inputs and/or outputs
#308 opened Nov 27, 2024 by niradsp
3
What does it say about our data that the m6a RNA modification rates seem somewhat low? question Looking for clarification on inputs and/or outputs
#307 opened Nov 27, 2024 by aleighbrown
4
High memory usage of modkit extract full troubleshooting workflow and data preparation questions
#306 opened Nov 27, 2024 by Shians
3
Question about the appropriate threshold for mod_qual question Looking for clarification on inputs and/or outputs
#305 opened Nov 25, 2024 by gyuhee0928
5
Entropy on strand enhancement New feature or request
#301 opened Nov 18, 2024 by Ge0rges
5
No methylation information was calculated for some reads troubleshooting workflow and data preparation questions
#299 opened Nov 13, 2024 by Wshengquan
3
Passing concated pileup to find-motifs question Looking for clarification on inputs and/or outputs
#298 opened Nov 12, 2024 by Ge0rges
2
Filtering accuracy question question Looking for clarification on inputs and/or outputs
#297 opened Nov 8, 2024 by Ge0rges
9
modkit extract full and modkit extract calls question Looking for clarification on inputs and/or outputs
#296 opened Nov 6, 2024 by Flower9618
3
Using segmenting on differential methylation question Looking for clarification on inputs and/or outputs
#295 opened Nov 5, 2024 by Raya-Faigenbaum-Romm
2
dmr multi will not create necessary directories bug Something isn't working troubleshooting workflow and data preparation questions
#294 opened Nov 5, 2024 by Yang990-sys
13
Documentation ambiguity documentation Improvements or additions to documentation
#293 opened Oct 31, 2024 by Ge0rges
1
how is calculate valid_coverage ? Different results between total read or subsample reads question Looking for clarification on inputs and/or outputs
#292 opened Oct 29, 2024 by DelphIONe
3
ProTip! Exclude everything labeled bug with -label:bug.