macs3 callpeak-t ChIP.bam-c Control.bam--broad-g hs--broad-cutoff0.1###ATAC-seq 的峰值识别(成对末端模式) macs3 callpeak-fBAMPE-tATAC.bam-g hs-n test-B-q0.01###ATAC-seq 的峰值识别(关注插入位点,使用单端模式) macs3 callpeak-fBAM-tATAC.bam-g hs-n test-B-q0.01--shift-50--ex...
macs3 callpeak-t ChIP.bam-c Control.bam--broad-g hs--broad-cutoff0.1###ATAC-seq 的峰值识别(成对末端模式) macs3 callpeak-fBAMPE-tATAC.bam-g hs-n test-B-q0.01###ATAC-seq 的峰值识别(关注插入位点,使用单端模式) macs3 callpeak-fBAM-tATAC.bam-g hs-n test-B-q0.01--shift-50--ex...
Discussed in #675 Originally posted by DayTimeMouse November 19, 2024 Hi, Thanks for developing this function to call peaks for ATAC-Seq. I ran macs3 hmmratac -i final.bam -n treat --cutoff-analysis-only. Then, I got the report(see the a...
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 file.bam -n file -f BAMPE --outdir ./dir --cutoff-analysis-on...
对于ATAC-seq双端数据的操作: macs3 callpeak -f BAMPE -t ATAC.bam -g hs -n test -B -q 0.01 -f是输入文件的格式,可以是BAM、BED,软件可以自动识别,但是需要注意自动识别是无法区分是PE还是SE,所以建议手动指定;-g是有效基因组大小,软件预设了模式物种的有效因组大小,如果hs人,mm小鼠;-n是样本名字...
MACS3 github专门开放了一个征对 ATAC-seq call peak 的讨论模块:https://github.com/macs3-project/MACS/discussions/435 image.png liu tao学生HMMRATAC开发者不同意xi chen说法:https://twitter.com/epigeneticsnerd/status/1337081681141002240 So if you are going to useMACS1/2forATAC-seq, andI will inste...
1. enable python3.13 test; 2. disable FRAG support for now for callpe… Feb 6, 2025 MACS3 enable FRAG support in callpeak and pileup Feb 16, 2025 bin enable FRAG support in callpeak and pileup Feb 16, 2025 conda/macs3 Update meta.yaml ...
1. enable python3.13 test; 2. disable FRAG support for now for callpe… Feb 6, 2025 MACS3 enable FRAG support in callpeak and pileup Feb 16, 2025 bin enable FRAG support in callpeak and pileup Feb 16, 2025 conda/macs3 Update meta.yaml ...
MACS -- Model-based Analysis of ChIP-Seq macs3-project.github.io/MACS/ Topics python dnase-seq chip-seq peak-caller atac-seq poisson-equation macs Resources Readme License BSD-3-Clause license Code of conduct Code of conduct Activity Custom properties Stars 724 stars Watchers 48...
I am trying to call peaks in ATAC-seq data. According to the documentation: To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5' ends of sequenced reads should be extended in both direction to smooth the p...