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modkit pileup --phased return only combined haplotype while processing whole genome
troubleshootingworkflow and data preparation questionsworkflow and data preparation questionsStatus: Open.#638 In nanoporetech/modkit;Does --single-code h perform 5hmC-vs-all or 5hmC-only DMR analysis?
documentationImprovements or additions to documentationImprovements or additions to documentationStatus: Open.#637 In nanoporetech/modkit;- Status: Open.#634 In nanoporetech/modkit;
compare-tx-sites multiple replicates per condition
enhancementNew feature or requestNew feature or requestStatus: Open.#633 In nanoporetech/modkit;Explanation for modkit stats output
questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputsStatus: Open.#631 In nanoporetech/modkit;modkit v0.6.3 error when running on remora generated modbam
enhancementNew feature or requestNew feature or requestStatus: Open.#630 In nanoporetech/modkit;Modkit pile up Inconsistent biological results for RNA m5c
Analysis QuestionHelp with analysis of base modification dataHelp with analysis of base modification dataStatus: Open.#628 In nanoporetech/modkit;Sample swap in modkit dmr compare-tx-sites
bugSomething isn't workingSomething isn't workingbuild-availablecustom build produced for fix.custom build produced for fix.Status: Open.#627 In nanoporetech/modkit;pileUp and dmr showing significant results for m6A even with very low amount of mapped reads from Dorado's modBAM
questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputsStatus: Open.#618 In nanoporetech/modkit;Cutoff Threshold Sensitivity in Human Samples
questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputsStatus: Open.#616 In nanoporetech/modkit;V0.6.1 does not work on pacbio samples, while v0.5.0 worked fine (no problems with ONT)
troubleshootingworkflow and data preparation questionsworkflow and data preparation questionsStatus: Open.#612 In nanoporetech/modkit;estimated pass threshold with default settings very high (v0.5.0 and v.0.6.1)
troubleshootingworkflow and data preparation questionsworkflow and data preparation questionsStatus: Open.#611 In nanoporetech/modkit;