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DNA Methylation data analysis using Winnowmap

Status: Open.

#58 In marbl/Winnowmap;

· msfalmeida opened on May 19, 2026

RNA-seq

Status: Open.

#57 In marbl/Winnowmap;

· franci-r opened on Apr 13, 2026

output SAM without header

Status: Open.

#55 In marbl/Winnowmap;

· orski-hryc opened on Dec 8, 2025

Parameters for accurate Oxford Nanopore reads

Status: Open.

#54 In marbl/Winnowmap;

· jyw-atgithub opened on Sep 19, 2025

Overflow issue on -K parameter

Status: Open.

#53 In marbl/Winnowmap;

· Yoonsung1203 opened on Jul 24, 2025

Question: Best practice for aligning reads against two highly similar genomes

Status: Open.

#51 In marbl/Winnowmap;

· jacgonisa opened on Mar 3, 2025

Winnowmap doesn't throw a [Warning] or [Error] when -W is empty

Status: Open.

#50 In marbl/Winnowmap;

· Isoris opened on Jan 31, 2025

Option to preserve MM/ML tags

Status: Open.

#48 In marbl/Winnowmap;

· aliceedoe opened on Sep 5, 2024

Sequence information not present in BAM file when mapping quality is 0 for a read

Status: Open.

#47 In marbl/Winnowmap;

· jagadhesh89 opened on Aug 30, 2024

ERROR: input list of k-mers and winnowmap parameter k are inconsistent

Status: Open.

#46 In marbl/Winnowmap;

· zhyx6511 opened on Jul 18, 2024

Seeing multiple primary alignments per read

Status: Open.

#44 In marbl/Winnowmap;

· mwykes opened on Feb 21, 2024

Detect deletion between gene and pseudogenes

Status: Open.

#42 In marbl/Winnowmap;

· keenhl opened on Nov 7, 2023