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macs3-project
MACS -- Model-based Analysis of ChIP-Seq
When calling peaks, will there be differences between the results obtained from split chromosomes and merged chromosomes?
**Describe the bug** I am running hmmratac on bulk ATAC-seq data. I am following the tutorial on your documentation site. The command reads all the BAM reads, but then dies...
This is a very minor issue but I thought I would report it. One can provide --hmm-type on the command line. I was surprised when I did this, that the...
Using the following call in MACS2: `macs2 callpeak -t {input} -f BAMPE -B -g hs --outdir peak_files/ -n {name}` MACS2 either stalls or presents an error message depending on whether...
hello Tao, @taoliu I was just wondering how to derive this LR formula. Can you please explain it in more details?  https://macs3-project.github.io/MACS/docs/bdgdiff.html Best,
The "Advanced Step-by-step peak calling using MACS3 commands" tutorial [[webpage](https://macs3-project.github.io/MACS/docs/Advanced_Step-by-step_Peak_Calling.html), [source](https://github.com/macs3-project/MACS/blob/master/docs/source/docs/Advanced_Step-by-step_Peak_Calling.md)] has 2 issues: 1. The tutorial claims that the 2 test files, CTCF_ChIP_200K.bed.gz and CTCF_Control_200K.bed.gz, can be found "in...
Hi, I have a big cohort of scATACseq data, totaling 1 billion fragments from 24 pools of experiments (24 billion total). I've been trying to run hmmratac on these 24...
Hi, I have run macs3 hmmratac with and without a blacklist and I have realised that even small blacklisted regions (~1kb long can lead to huge gaps in the peak...
Hello, I'm trying to install MACS on my Linux system using "pip3 install macs3" code , but I got the error. Defaulting to user installation because normal site-packages is not...
Hello, I would like to use the MACS3 hmmratac tool to peak call my 10x multiome (single-cell ATAC-seq) dataset. I firstly ran the cutoff analysis as follows: `macs3 hmmratac -i...
