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Issues list

ATAC-seq settings General Question
#145 opened Aug 31, 2016 by igordot
29
Q: How to incorporate ChIP-seq spike in normalisation into peak calling? General Question
#356 opened Jan 15, 2020 by tudumanne
@taoliu
26
Errors out at peak calling
#122 opened Mar 16, 2016 by blikzen
21
Bug: floating point rounding discrepancies on some architectures Bug Report
#359 opened Feb 18, 2020 by tillea
@taoliu
18
Bug: Callvar throws an error when run on broadPeak file Bug Report
#643 opened May 2, 2024 by LinearParadox
@taoliu
15
Bug: HMMRATAC ends in ZeroDivisionError: float division Bug Report
#531 opened Oct 24, 2022 by lionaid
11
Q: HMMRATAC producing too many peaks General Question
#636 opened Apr 3, 2024 by igordot
10
Q: Using MACS2 callpeak for bacteria ChIP-Seq data with --keep-up 1 reports too few paired peaks General Question
#353 opened Jan 11, 2020 by huizhen2014
10
Q: MACS2 parameter for ATAC-seq, BAMPE or single-end mode General Question
#331 opened Oct 19, 2019 by yue131
@taoliu
9
Running MACS2 on RNA-Seq BAM files
#186 opened Apr 12, 2017 by gireeshkbogu
9
Question about calling differential binding events
#156 opened Oct 12, 2016 by toxin08x
8
Q: What parameters would you recommend optimizing, and what could be the reason for some peaks not being called? General Question
#391 opened May 12, 2020 by eregenyi
@taoliu
7
local variable 'dup_locs' referenced before assignment
#153 opened Oct 3, 2016 by vsvinti
7
Bug: test/test_Signal.py:51: AssertionError 162 != 161 with Python 3.7 & MACS 2.2.5 Bug Report
#340 opened Oct 31, 2019 by mr-c
@taoliu
6
Q: Limit number of threads General Question
#238 opened May 1, 2018 by dwesche
6
ATAC-Seq parameters
#195 opened May 31, 2017 by firatuyulur
6
pair-ended data in BAMPE and BEDPE do not produce the same results
#183 opened Apr 6, 2017 by MariusGheorghe
6
Missing summit location when run macs2 with --broad option
#177 opened Mar 21, 2017 by AlicePsyche
6
Q: question about the libmvec.so.1 error. General Question
#604 opened Dec 4, 2023 by Simple53
5
hmmratac adjust means and standard deviation Bug Report
#593 opened Aug 31, 2023 by LinearParadox
5
Bug: variable overflow in peak column of narrowPeak file Bug Report
#500 opened Feb 1, 2022 by diego-rt
5
macs2 callpeak option about effective genome size and shift model General Question
#463 opened May 24, 2021 by LunaPatton
5
Q: Peakcalling in paired-end bam as single-end and keeping all reads Feature Request General Question
#421 opened Nov 5, 2020 by MbDiop
@taoliu
5
Q: Why cannot you not set --extsize to 0? General Question
#411 opened Sep 3, 2020 by sklasfeld
5
No common chromosome names can be found from treatment and control! Check your input files! MACS will quit...
#266 opened Oct 24, 2018 by EPKok
5
ProTip! What’s not been updated in a month: updated:<2025-01-13.