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...
used for ChIP-Seq data alone, or with a control sample with the increase of specificity. Moreover, as a general peak-caller, MACS can also be applied to any "DNA enrichment assays" if the question to be asked is simply:where we can find significant reads coverage than the random back...
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...
v3.0.3 Changes for MACS (3.0.3) Features added Now support FRAG format forsingle-cell ATAC-seqincallpeakand pileup. FRAG format is used by 10x Genomics to store alignments from the single-cell ATAC-seq pipelinecellranger-atacor the multi-omics...
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...
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...
I am running MACS3 on some ATACseq data collected from T cells treated with shRNAmir's for various genes. I'm supplying multiple control and treatment files, and use the callpeaks command to generate .narrowpeak files. However, I am noti...
Hi, I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally open regions. Can you please explain why m...