Discussions

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  running MACS3 with multiple input file and cell barcodes

  chrysania asked Jan 23, 2026 in Q&A · Unanswered

  

  

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  MACS3 HMMRATAC Peak Calling Cutoff parameters?

  budeer asked May 12, 2025 in Q&A · Unanswered

  

  

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  Why scaling the smaller dataset to the same depth as the larger dataset results in more false positive peaks.

  bentyeh started Feb 27, 2025 in Show and tell

  

  

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  numpy 2 compatibility

  jeanmonet started Feb 7, 2025 in General · Closed

  

  

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  Types of emissions for the Hidden Markov Model

  igordot asked Feb 12, 2025 in Q&A · Unanswered

  

  

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  Strange results with peakcall

  moshe-olshansky asked Jan 23, 2025 in Q&A · Unanswered

  

  

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  About ATAC-seq call peak (hmmratac) and differential analysis via MACS3

  DayTimeMouse asked Nov 19, 2024 in Q&A · Unanswered

  

  

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  Call peaks on modified pileup file, instead of calling on modified BAMPE file

  jeanmonet asked Sep 15, 2024 in Q&A · Unanswered

  

  

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  error: subprocess-exited-with-error Getting requirements to build wheel did not run successfully.

  timeisno asked Sep 26, 2024 in Q&A · Unanswered

  

  

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  Where can I download MACS3 v3.0.2 from?

  kate-wa asked Jun 13, 2024 in Q&A · Answered

  

  

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  ERROR: Could not build wheels for MACS2, which is required to install pyproject.toml-based projects

  aperreault started Jul 17, 2023 in General

  

  

  

  

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  MAC2 output of bdg file contain only called peaks/reads information or all mapped reads?

  TingtingSsl2 started Apr 26, 2024 in General

  

  

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  Command line to use HMMRATAC in MACS3

  tahirsajid asked Jan 11, 2023 in Q&A · Unanswered

  

  

  

  

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  ATAC-seq peak calling

  igordot asked Dec 10, 2020 in Q&A · Unanswered

  

  

  

  

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  Using MACS for RIP-seq analysis

  maria123701 asked Nov 30, 2023 in Q&A · Unanswered

  

  

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  [ERROR] Input bam file was read incompletely during peak calling

  guodong1988 started Aug 11, 2023 in General

  

  

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  [Question]: What is recommended command line for ATAC-Seq peak calling with bams from Paired End data

  tamuanand asked Jul 24, 2023 in Q&A · Unanswered

  

  

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  Unclear Application of Algorithm to Single Cell CUT&Tag or CUT&RUN Data

  DarioS started Mar 29, 2023 in General

  

  

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  MACS3 - custom genome

  PycnopodiaD started Oct 15, 2022 in General

  

  

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  Calculation of λ for no crontrol samples (ATAC seq)

  tahirsajid started Mar 20, 2023 in Ideas

  

  

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  MACS3 TypeError: an integer is required

  luised94 asked Sep 19, 2022 in Q&A · Unanswered

  

  

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  python-dev prerequisite

  lisaxplin started Jun 29, 2022 in General

  

  

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  How does MACS deal with read pairs that only have one read aligned in the peak region?

  alexanderkzee asked Jan 26, 2022 in Q&A · Unanswered

  

  

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  MACS3 or 2 for production?

  douglas-hoen started Dec 9, 2021 in General

  

  

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  How should I process a chip-seq data that each sample with a input by macs2

  ryrl9703 asked Oct 26, 2021 in Q&A · Unanswered

  

  

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