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How to carryout gene annotation with *.bedmethyl.gz and reference.gtf file ?

Status: Open.

#559 In nanoporetech/modkit;

· vaishnavpvarma opened on Dec 27, 2025

Documentation request for <code>dmr</code> technique and console messages

Status: Open.

#558 In nanoporetech/modkit;

· SuhasSrinivasan opened on Dec 26, 2025

--motif % 0 and --ignore % not working as expected?

Status: Open.

#557 In nanoporetech/modkit;

· CarolinaA09 opened on Dec 22, 2025

<code>modkit pileup</code> --bgzf but output not compressed

bugSomething isn't workingSomething isn't working

Status: Open.

#556 In nanoporetech/modkit;

· jkh00 opened on Dec 19, 2025

modkit dmr pair fails with Error: “valid coverage is not equal to the sum of canonical and modified counts”

bugSomething isn't workingSomething isn't working

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#554 In nanoporetech/modkit;

· NathaneilKnight opened on Dec 15, 2025

Help understanding motif search with --known-motif

bugSomething isn't workingSomething isn't working

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#553 In nanoporetech/modkit;

· ndusek opened on Dec 11, 2025

Motif specific, polyploid DMR analysis?

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#551 In nanoporetech/modkit;

· jkh00 opened on Dec 9, 2025

Discrepancy between threshold estimated by modkit summary and modkit pileup and modkit sample-probs

enhancementNew feature or requestNew feature or request

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#550 In nanoporetech/modkit;

· guanhomer opened on Dec 7, 2025

Discrepancy between threshold estimated by modkit summary and modkit pileup

troubleshootingworkflow and data preparation questionsworkflow and data preparation questions

Status: Open.

#548 In nanoporetech/modkit;

· gsukrit opened on Dec 5, 2025

Modkit pileup (v. 0.6.0) - modification percentage over 100%

bugSomething isn't workingSomething isn't working

build-availablecustom build produced for fix.custom build produced for fix.

Status: Open.

#547 In nanoporetech/modkit;

· SimonBache opened on Dec 4, 2025

MAP QUALITY Filter Request

enhancementNew feature or requestNew feature or request

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#546 In nanoporetech/modkit;

· haileye4 opened on Dec 2, 2025

Feature request: downsampling to X reads

questionLooking for clarification on inputs and/or outputsLooking for clarification on inputs and/or outputs

Status: Open.

#542 In nanoporetech/modkit;

· billytcl opened on Nov 24, 2025