Issues

• File name restrictions for genome parameter

  StevenWingett/HiCUP#106 · Filter by author bernt-matthias opened on May 21, 2026
  1

• Issue with HiCUP 0.9.2 output format and compatibility with HiCExplorer

  StevenWingett/HiCUP#104 · Filter by author JeasonHe-Bot opened on May 17, 2025
  2

• Speed up scripts

  StevenWingett/HiCUP#102 · Filter by author Ethan-Fu-2000 opened on Jun 13, 2024
  1

• hicup deduplicator error in read.table function

  StevenWingett/HiCUP#101 · Filter by author WeiCSong opened on Feb 22, 2024
  2

• hicup2homer error in converting HiCPro bam file

  StevenWingett/HiCUP#98 · Filter by author Lei-Guo opened on Dec 27, 2023
  10

• Add comb_dedup and HiCUP integrity checker scripts to Misc folder

  enhancement
  StevenWingett/HiCUP#94 · Filter by author StevenWingett opened on Aug 1, 2023

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

  StevenWingett/HiCUP#92 · Filter by author jyaomda opened on Jun 27, 2023
  4

• Truncation at very start of sequence.

  StevenWingett/HiCUP#62 · Filter by author StephenRicher opened on Jan 4, 2022
  1

• Display percentages in HTML report

  StevenWingett/HiCUP#50 · Filter by author StevenWingett opened on Mar 18, 2021

• HiCUP report di-tag size plot

  bugnecessary improvement
  StevenWingett/HiCUP#49 · Filter by author StevenWingett opened on Mar 5, 2021
  2

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

  necessary improvement
  StevenWingett/HiCUP#48 · Filter by author StevenWingett opened on Mar 1, 2021
  7

• SAM flags could be improved?

  question
  StevenWingett/HiCUP#43 · Filter by author StevenWingett opened on Oct 26, 2020

• NlaIII digestion problem

  bug
  StevenWingett/HiCUP#39 · Filter by author StevenWingett opened on Sep 29, 2020
  3

• DNase compatibility

  potential enhancement
  StevenWingett/HiCUP#37 · Filter by author StevenWingett opened on Aug 13, 2020
  2

• Using hicup_deduplicator more than once

  necessary improvement
  StevenWingett/HiCUP#36 · Filter by author StevenWingett opened on Jul 29, 2020

• Bowtie2 Failing?

  bug
  StevenWingett/HiCUP#31 · Filter by author StevenWingett opened on Jul 7, 2020
  1

• Error when passing HiCUP parameters via command line

  someone else's problem (reported)
  StevenWingett/HiCUP#23 · Filter by author StevenWingett opened on Jun 9, 2020
  1

• Processing "multi"-tag reads

  enhancement
  StevenWingett/HiCUP#22 · Filter by author StevenWingett opened on Jun 8, 2020
  1

• Arima cut sites

  question
  StevenWingett/HiCUP#20 · Filter by author StevenWingett opened on May 18, 2020

• Add to DockerHub / Anaconda

  enhancement
  StevenWingett/HiCUP#17 · Filter by author StevenWingett opened on May 14, 2020
  1

• Integrate the capture script into main pipeline

  enhancement
  StevenWingett/HiCUP#16 · Filter by author StevenWingett opened on May 14, 2020
  1

• Write out BAM file of muti-mapping reads for Bori for next update

  enhancement
  StevenWingett/HiCUP#7 · Filter by author StevenWingett opened on Jul 3, 2019

• Add R and Y in digester script

  enhancement
  StevenWingett/HiCUP#4 · Filter by author StevenWingett opened on Feb 11, 2019
  1