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Discrepency Between Methylated_Sites.tsv and motifs.tsv

Status: Open.

#46 In cultivarium/MicrobeMod;

· Ryan-Kich opened on Apr 20, 2026

Calling methylation for small plasmids

Status: Open.

#45 In cultivarium/MicrobeMod;

· KuroRiposte opened on Mar 11, 2026

Installation broken because of meme

Status: Open.

#43 In cultivarium/MicrobeMod;

· winterlich opened on Oct 12, 2025

problem with modkit pileup

Status: Open.

#42 In cultivarium/MicrobeMod;

· paulinecoulon opened on Jul 31, 2025

Different results than REBASE?

Status: Open.

#41 In cultivarium/MicrobeMod;

· Ge0rges opened on Jul 23, 2025

pytest failed: IndexError: tuple index out of range

Status: Open.

#40 In cultivarium/MicrobeMod;

· Zick007 opened on Jun 30, 2025

Providing our own modkit pileup output for MicrobeMod downstream processing?

Status: Open.

#38 In cultivarium/MicrobeMod;

· naturepoker opened on Jun 6, 2025

STREME motif Missing from MicrobeMod Output

Status: Open.

#36 In cultivarium/MicrobeMod;

· nhinvo opened on Apr 3, 2025

Silent output

Status: Open.

#35 In cultivarium/MicrobeMod;

· Ge0rges opened on Feb 24, 2025

Identification of motifs fails with lower-case fasta reference sequences

Status: Open.

#29 In cultivarium/MicrobeMod;

· tfwulff opened on Sep 14, 2024

help with troubleshooting the error

Status: Open.

#27 In cultivarium/MicrobeMod;

· yklight1 opened on Jul 19, 2024

--percent_cutoff_streme parameter changes _methylated_sites.tsv output

Status: Open.

#23 In cultivarium/MicrobeMod;

· winterlich opened on Mar 14, 2024