StevenWingett/HiCUP

Issues

• Speed up scripts

  #102 opened 6 months ago by fys666
  1

• hicup deduplicator error in read.table function

  #101 opened 10 months ago by WeiCSong
  2

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

  #48 opened 4 years ago by StevenWingett
  7

• hicup2homer error in converting HiCPro bam file

  #98 opened a year ago by Lei-Guo
  10

• NlaIII digestion problem

  #39 opened 4 years ago by StevenWingett
  3

• Trimming step before HiCUP?

  #99 opened a year ago by iagooteroc
  1

• HiCUP Truncater incorrect input

  #97 opened a year ago by jmtobin257
  0

• fileNamer error for genome indices

  #96 opened a year ago by kaileeyoshimura
  5

• New issue encountered

  #95 opened a year ago by Nandhininj
  1

• Merge parallel jobs from the same sample?

  #93 opened a year ago by SalvadorGJ
  1

• Add comb_dedup and HiCUP integrity checker scripts to Misc folder

  #94 opened a year ago by StevenWingett
  0

• Error encountered while working on HiCUP

  #91 opened a year ago by Nandhininj
  1

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

  #92 opened a year ago by jyaomda
  4

• How to specify the bowtie2 option

  #90 opened 2 years ago by TakatoG
  1

• Change version

  #86 opened 2 years ago by lldelisle
  3

• create_baitmap_rmap.pl

  #77 opened 2 years ago by TakatoG
  3

• `scribl_capture_ditag_sorter.pl` seems to be in dos

  #82 opened 2 years ago by lldelisle
  1

• hicup2homer is not executable in v0.9.0

  #81 opened 2 years ago by lldelisle
  1

• Update documentation

  #21 opened 2 years ago by StevenWingett
  5

• Add Scribler to the HiCUP Misc folder

  #56 opened 2 years ago by StevenWingett
  1

• R error?

  #76 opened 2 years ago by TakatoG
  2

• index error

  #75 opened 2 years ago by TakatoG
  2

• How to merge data from multiple lanes or bological replicates

  #74 opened 2 years ago by HammadFarooq
  1

• How to use the outputfile hicup.bam to run 3ddna

  #73 opened 2 years ago by Biscuite-wzy
  4

• Why not use BWA mem as a mapper?

  #72 opened 2 years ago by joshuak94
  1

• Multi-thread option for Hicup filter and deduplicator.

  #71 opened 2 years ago by Shubhamverma-bioinfo
  1

• what is the difference between hicup.bam and pair.bam? Why not all files will produce hicup.bam?

  #69 opened 2 years ago by xsq2022
  2

• Summary report file

  #68 opened 2 years ago by Oksanak22
  7

• HiCUP error after pairing - Error in read.table/no lines available in input/Could not produced hicup_mapper summary/fail to read the header from "pair.bam"

  #67 opened 3 years ago by matteozoia4
  6

• Error in pairing while running hicup_mapper

  #66 opened 3 years ago by Giuseppe1995
  2

• how to chose --format option while running hicup_mapper

  #65 opened 3 years ago by Giuseppe1995
  2

• Truncation of 3' Partial Ligation Sequences

  #63 opened 3 years ago by StephenRicher
  4

• HiCUP report di-tag size plot

  #49 opened 4 years ago by StevenWingett
  2

• Truncation at very start of sequence.

  #62 opened 3 years ago by StephenRicher
  1

• UMIs incorporated into deduplicator

  #61 opened 3 years ago by aturocks
  26

• di-tag parameter

  #60 opened 3 years ago by ivyhzau
  3

• Hicup capture script not working

  #59 opened 3 years ago by aturocks
  3

• cut site

  #51 opened 3 years ago by mfazel
  3

• hicup_reporter can't run if it detects other previous reports

  #58 opened 3 years ago by LaureTomas
  5

• Tutorial test data not pairing with HiCUP Mapper after bowtie2 alignment

  #57 opened 3 years ago by aturocks
  3

• Bowtie2 Failing?

  #31 opened 4 years ago by StevenWingett
  1

• Potential Bowtie2 error?

  #55 opened 3 years ago by Axolotl233
  1

• link for HiCUP v0.5.3

  #52 opened 3 years ago by ivyhzau
  1

• Display percentages in HTML report

  #50 opened 4 years ago by StevenWingett
  0

• SAM flags could be improved?

  #43 opened 4 years ago by StevenWingett
  0

• Add documentation to pipeline combinations branch in separate repo

  #38 opened 4 years ago by StevenWingett
  1

• DNase compatibility

  #37 opened 4 years ago by StevenWingett
  0

• Using hicup_deduplicator more than once

  #36 opened 4 years ago by StevenWingett
  0

• Processing "multi"-tag reads

  #22 opened 5 years ago by StevenWingett
  1

• Error when passing HiCUP parameters via command line

  #23 opened 5 years ago by StevenWingett
  1