Issues

• Is trimming needed before running the pipeline?

  ENCODE-DCC/chip-seq-pipeline2#315 · Filter by author gilgolan73 opened on Oct 9, 2025

• tss dataset for mm10

  ENCODE-DCC/chip-seq-pipeline2#314 · Filter by author nyanmo opened on Jul 16, 2025

• peak list have peaks with FDR greater than 0.01

  ENCODE-DCC/chip-seq-pipeline2#313 · Filter by author cxtaslim opened on Apr 4, 2025

• Repeated files and reusing input and filtered data

  ENCODE-DCC/chip-seq-pipeline2#312 · Filter by author jamesaliba opened on Mar 27, 2025

• macs2 bedgraphs

  ENCODE-DCC/chip-seq-pipeline2#311 · Filter by author giardine opened on Mar 17, 2025

• Question regarding final peak list

  ENCODE-DCC/chip-seq-pipeline2#310 · Filter by author cxtaslim opened on Mar 10, 2025

• Question regarding samples

  ENCODE-DCC/chip-seq-pipeline2#309 · Filter by author cxtaslim opened on Mar 3, 2025
  2

• Insufficient peaks in pseudoreplicates resulting in chip.idr_ppr failure

  ENCODE-DCC/chip-seq-pipeline2#307 · Filter by author nursyahr opened on Sep 18, 2024

• Can chip-seq-pipeline2 run locally without internet?

  ENCODE-DCC/chip-seq-pipeline2#306 · Filter by author cyz0315 opened on Jun 26, 2024
  1

• Datasets for TF-target genes

  ENCODE-DCC/chip-seq-pipeline2#305 · Filter by author yiqisu opened on Mar 19, 2024

• pipeline stuck in call-macs2_signal_track_pooled

  ENCODE-DCC/chip-seq-pipeline2#302 · Filter by author Cmfffff opened on Jan 11, 2024

• How do you resume ?

  ENCODE-DCC/chip-seq-pipeline2#301 · Filter by author olechnwin opened on Oct 27, 2023

• missing slurm qos parameter

  ENCODE-DCC/chip-seq-pipeline2#300 · Filter by author giardine opened on Oct 13, 2023
  2

• how to create pseudo-replicate files

  ENCODE-DCC/chip-seq-pipeline2#299 · Filter by author songxh1996 opened on Sep 22, 2023
  1

• Does the calculation of sval in encode_task_macs2_signal_track_chip.py take into account the difference between single-end and paired-end data?

  ENCODE-DCC/chip-seq-pipeline2#298 · Filter by author ezioljj opened on Sep 1, 2023
  2

• signal track height is higher for input control

  ENCODE-DCC/chip-seq-pipeline2#297 · Filter by author jamesaliba opened on May 20, 2023
  1

• no motif output

  ENCODE-DCC/chip-seq-pipeline2#296 · Filter by author jamesaliba opened on May 20, 2023

• The pipeline stops at Job chip.read_genome_tsv

  ENCODE-DCC/chip-seq-pipeline2#295 · Filter by author peculiar97 opened on May 19, 2023
  10

• Fixed peak size

  ENCODE-DCC/chip-seq-pipeline2#294 · Filter by author kbattenb opened on Apr 17, 2023
  1

• ”caper init local“ error

  ENCODE-DCC/chip-seq-pipeline2#293 · Filter by author songxh1996 opened on Apr 5, 2023
  3

• caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1

  ENCODE-DCC/chip-seq-pipeline2#292 · Filter by author zh3li opened on Feb 23, 2023
  2

• Changing MACS2 output from earlier pipeline version

  ENCODE-DCC/chip-seq-pipeline2#291 · Filter by author clarabakker opened on Jan 25, 2023
  2

• Conflicts while running scripts/install_conda_env.sh

  ENCODE-DCC/chip-seq-pipeline2#285 · Filter by author agduncan94 opened on Aug 17, 2022
  3

• HELP: call-xcor fails with TEST command

  ENCODE-DCC/chip-seq-pipeline2#284 · Filter by author yinyeya opened on Jun 20, 2022
  3

• Are adapter-trimmed FASTQs required?

  ENCODE-DCC/chip-seq-pipeline2#283 · Filter by author benayang opened on Jun 14, 2022
  3