MACS
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macs3-project
MACS -- Model-based Analysis of ChIP-Seq
I wanted to test macs3 for genomic peaks detection. For that, a number of reads obtained from Pacbio, previously aligned and subsequently sorted and indexed has been provided for macs3....
Is it possible to implement a --call-summits feature in MACS3 bdgpeakcall? Is it possible to deconvolve subpeaks within the narrowpeak called by the bdgpeakcall? Thanks!
Unsure if this should be listed as bug or question, but it feels like something isn't working properly to me so I listed it as bug. From the docs: "The...
I'm trying to run hmmratac to call peaks from my bampe files the code I used is hmmratac -i Alignments/file.bam -f BAMPE --outdir Peaks/ -n name It runs for a...
**Use case** Hello I want to do peak calling on my ATAC seq data, and for that I use, callpeak and hmmratac. **Describe the problem** My problem here is with...
I'm trying to run bdgcmp on some spike-in normalised bedGraphs I've generated used MACS3 tools. Here is the command line I'm running: `macs3 bdgcmp -m qpois -t DATA/BED/TEAD1/TEAD1_T1_pos_1_pileup_GRCh38_sort_spikeBDGP6.32_pe.bedGraph -c DATA/BED/TEAD1/Input_T1_pos_pe_pileup_sort_norm10M_nozero.bedGraph...
Error message below (bottom): INFO @ 21 Oct 2024 16:38:48: [107 MB] # Command line: hmmratac -i BED_files_sorted/9.bedpe -f BEDPE -n macs3_output/9 # Random seed selected as: 10151 # Use...
AFAIK the peak caller operates sequentially on each chromosome. I believe the process can be parallelized by calling peaks in a separate process for each chromosome (up to a certain...
**Describe the bug** I updated to the last version of MACS3 (3.0.2) and now I get this error whenever I run the program: /tmp/slurmd/job1000362/slurm_script: line 105: 138001 Illegal instruction (core...
I came across several posts that the MACS is not fine-tuned for Viral ChipSeq (eg SARS-CoV2) (See [Post1](https://www.biostars.org/p/348105/), [Post2](https://biostar.galaxyproject.org/p/17895/). What parameters do you think needs to be adjusted to get...
