Issues

• Footprint symmetry score

  fl-yu/CUT-RUNTools-2.0#88 · Filter by author ChelseaCHENX opened on Nov 4, 2025

• environment yml file issue

  fl-yu/CUT-RUNTools-2.0#87 · Filter by author christinaruilin opened on Oct 1, 2025

• no bigwig file; cannot stat

  fl-yu/CUT-RUNTools-2.0#86 · Filter by author thugib opened on Apr 10, 2025
  4

• Single end fastq file as input?

  fl-yu/CUT-RUNTools-2.0#83 · Filter by author pc2001 opened on Sep 6, 2024

• about Configuration file (bulk-config.json)

  fl-yu/CUT-RUNTools-2.0#82 · Filter by author ajcorriaosorio opened on May 9, 2024

• Issues in SEACR_1.1.sh file

  fl-yu/CUT-RUNTools-2.0#81 · Filter by author saimaniharreddy opened on Mar 5, 2024

• Installation of R packages

  fl-yu/CUT-RUNTools-2.0#80 · Filter by author cnyongjun opened on Feb 16, 2024
  1

• Picard file error

  fl-yu/CUT-RUNTools-2.0#79 · Filter by author Shivani-kushwaha opened on Jan 7, 2024

• meme problen：Failed to create PNG file；make_cut_matrix mistake

  fl-yu/CUT-RUNTools-2.0#78 · Filter by author Zhiyi-Chen17 opened on Nov 13, 2023
  1

• SEACR input and spike-in normalization

  fl-yu/CUT-RUNTools-2.0#77 · Filter by author jordan841220 opened on Sep 8, 2023

• header of the produced file in bam is wrong

  fl-yu/CUT-RUNTools-2.0#75 · Filter by author sunta3iouxos opened on Aug 2, 2023

• space in the path brakes the script

  fl-yu/CUT-RUNTools-2.0#74 · Filter by author sunta3iouxos opened on Jul 10, 2023

• gff2bed: line 132: convert2bed: command not found

  fl-yu/CUT-RUNTools-2.0#73 · Filter by author sunta3iouxos opened on Jul 5, 2023

• ghostscript is not found

  fl-yu/CUT-RUNTools-2.0#72 · Filter by author sunta3iouxos opened on Jul 5, 2023
  1

• has the support for cutandrun software ended?

  fl-yu/CUT-RUNTools-2.0#71 · Filter by author sunta3iouxos opened on Jul 5, 2023
  1

• errror installing sexpdata

  fl-yu/CUT-RUNTools-2.0#70 · Filter by author sunta3iouxos opened on Jun 29, 2023

• A question about the +4 and -5 shifts

  fl-yu/CUT-RUNTools-2.0#69 · Filter by author bio-lilin opened on Jun 27, 2023
  1

• Interpretation of the cut site probability plot from fimo analysis

  fl-yu/CUT-RUNTools-2.0#66 · Filter by author HaniceSun opened on Apr 12, 2023

• Syntax of the if statements on the sh scripts

  fl-yu/CUT-RUNTools-2.0#64 · Filter by author ericpalto opened on Jan 31, 2023
  1

• other genome assembly

  fl-yu/CUT-RUNTools-2.0#63 · Filter by author jamesc99 opened on Oct 22, 2022

• pipeline questions: control sample and rerun skipping steps

  fl-yu/CUT-RUNTools-2.0#62 · Filter by author gianfilippo opened on Oct 13, 2022

• updated meme release

  fl-yu/CUT-RUNTools-2.0#61 · Filter by author gianfilippo opened on Oct 13, 2022

• Experimental controls

  fl-yu/CUT-RUNTools-2.0#59 · Filter by author brindabhatt opened on Aug 15, 2022

• Couldn't run with 'frag_120: FALSE'

  fl-yu/CUT-RUNTools-2.0#38 · Filter by author jamesc99 opened on Mar 15, 2022
  2

• how to interpret the parameter "fastq_sequence_length"

  fl-yu/CUT-RUNTools-2.0#31 · Filter by author fanzheng10 opened on Dec 4, 2021
  1