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high %failed_to_align reads

Status: Open.

#105 In StevenWingett/HiCUP;

· asaki1986 opened on Feb 9, 2026

Issue with HiCUP 0.9.2 output format and compatibility with HiCExplorer

Status: Open.

#104 In StevenWingett/HiCUP;

· JeasonHe-Bot opened on May 17, 2025

Speed up scripts

Status: Open.

#102 In StevenWingett/HiCUP;

· fys666 opened on Jun 13, 2024

hicup deduplicator error in read.table function

Status: Open.

#101 In StevenWingett/HiCUP;

· WeiCSong opened on Feb 22, 2024

hicup2homer error in converting HiCPro bam file

Status: Open.

#98 In StevenWingett/HiCUP;

· Lei-Guo opened on Dec 27, 2023

Add comb_dedup and HiCUP integrity checker scripts to Misc folder

enhancementNew feature or requestNew feature or request

Status: Open.

#94 In StevenWingett/HiCUP;

· StevenWingett opened on Aug 1, 2023

ERROR: The restriction site (re1) needs to be a valid DNA sequence

Status: Open.

#92 In StevenWingett/HiCUP;

· jyaomda opened on Jun 27, 2023

Truncation at very start of sequence.

Status: Open.

#62 In StevenWingett/HiCUP;

· StephenRicher opened on Jan 4, 2022

Display percentages in HTML report

Status: Open.

#50 In StevenWingett/HiCUP;

· StevenWingett opened on Mar 18, 2021

HiCUP report di-tag size plot

bugSomething isn't workingSomething isn't working

necessary improvementNot a bug, but the code needs improving in some wayNot a bug, but the code needs improving in some way

Status: Open.

#49 In StevenWingett/HiCUP;

· StevenWingett opened on Mar 5, 2021

HiCUP output if Tidyverse, Plotly and/or Pandoc not installed

necessary improvementNot a bug, but the code needs improving in some wayNot a bug, but the code needs improving in some way

Status: Open.

#48 In StevenWingett/HiCUP;

· StevenWingett opened on Mar 1, 2021

SAM flags could be improved?

questionFurther information is requestedFurther information is requested

Status: Open.

#43 In StevenWingett/HiCUP;

· StevenWingett opened on Oct 26, 2020