fl-yu/CUT-RUNTools-2.0

Issues

• TabError in validate.py

  #68 opened a month ago by pseudacriscrucifer
  3

• Single end fastq file as input?

  #83 opened 7 months ago by pc2001
  0

• about Configuration file (bulk-config.json)

  #82 opened a year ago by ajcorriaosorio
  0

• Issues in SEACR_1.1.sh file

  #81 opened a year ago by saimaniharreddy
  0

• Installation of R packages

  #80 opened a year ago by cnyongjun
  1

• Picard file error

  #79 opened a year ago by Shivani-kushwaha
  0

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

  #78 opened a year ago by Zhiyi-Chen17
  1

• adaptor fasta

  #46 opened 3 years ago by Yuling-Zhao
  6

• Error when generating bigwig format

  #56 opened 3 years ago by baijiexu
  9

• `jq` not listed as dependency

  #40 opened 3 years ago by quantumdot
  3

• has the support for cutandrun software ended?

  #71 opened 2 years ago by sunta3iouxos
  1

• SEACR input and spike-in normalization

  #77 opened 2 years ago by jordan841220
  0

• ghostscript is not found

  #72 opened 2 years ago by sunta3iouxos
  1

• deleted

  #76 opened 2 years ago by pc2001
  0

• header of the produced file in bam is wrong

  #75 opened 2 years ago by sunta3iouxos
  0

• A question about the +4 and -5 shifts

  #69 opened 2 years ago by bio-lilin
  1

• space in the path brakes the script

  #74 opened 2 years ago by sunta3iouxos
  0

• gff2bed: line 132: convert2bed: command not found

  #73 opened 2 years ago by sunta3iouxos
  0

• how to interpret the parameter "fastq_sequence_length"

  #31 opened 3 years ago by fanzheng10
  1

• empty trim2 directory

  #48 opened 3 years ago by Yuling-Zhao
  5

• errror installing sexpdata

  #70 opened 2 years ago by sunta3iouxos
  0

• Interpretation of the cut site probability plot from fimo analysis

  #66 opened 2 years ago by HaniceSun
  0

• Feature Request: Support for S3

  #51 opened 2 years ago by rmarable
  1

• Please improve error reporting with 'validate.py'

  #53 opened 2 years ago by rmarable
  1

• Some Python scripts are not executable

  #52 opened 2 years ago by rmarable
  1

• Syntax of the if statements on the sh scripts

  #64 opened 2 years ago by ericpalto
  1

• other genome assembly

  #63 opened 2 years ago by jamesc99
  0

• pipeline questions: control sample and rerun skipping steps

  #62 opened 2 years ago by gianfilippo
  0

• updated meme release

  #61 opened 2 years ago by gianfilippo
  0

• Mapping multiple lane for bulk

  #60 opened 3 years ago by nandankita
  1

• Experimental controls

  #59 opened 3 years ago by brindabhatt
  0

• singularity container run_bulkModule.sh script fails

  #55 opened 3 years ago by ponomarevsy
  24

• validate.py throws TabError with python3.6.0, replaced tabs with spaces

  #36 opened 3 years ago by kindln
  1

• Conda environment documentation reports inconsistent versions

  #54 opened 3 years ago by rmarable
  1

• Questions about process debugging

  #44 opened 3 years ago by songrunxian
  7

• Can't run single-cell example

  #47 opened 3 years ago by plbaldoni
  2

• inquire about trim adapter

  #49 opened 3 years ago by jamesc99
  2

• Samview failed to read header

  #50 opened 3 years ago by PatrickMaclean
  3

• KSEQ trouble

  #43 opened 3 years ago by itstomfrancis
  1

• Permission denied thrown in bulk-pipeline.sh

  #42 opened 3 years ago by quantumdot
  1

• Questions about motif discovery section under bulk-pipeline.sh

  #45 opened 3 years ago by mk1209567
  1

• paths in bulk-config.jason file

  #39 opened 3 years ago by thugib
  1

• Can CUT-RUNTools be used with Arabidopsis ?

  #41 opened 3 years ago by thugib
  1

• Alignment Error

  #30 opened 3 years ago by jamesc99
  3

• Couldn't run with 'frag_120: FALSE'

  #38 opened 3 years ago by jamesc99
  2

• About filteration of fragmeng length and reads shifting

  #37 opened 3 years ago by Liangyan-1996
  2

• Can't find index GATA1_D7_30min_chr11.bam

  #35 opened 3 years ago by litd
  1

• No read in trimmed2 can align to the reference genome

  #34 opened 3 years ago by Liangyan-1996
  5

• Problems in “dreme-py3” and “Making cut point matrix”

  #33 opened 3 years ago by Liangyan-1996
  2

• dreme problem

  #32 opened 3 years ago by Liangyan-1996
  1