Because, as it turns out, thesummit of an ATAC peak is the footprint. We also show this in the **HMMRATAC **paper. So if you are going to useMACS1/2forATAC-seq, andI will instead recommend using HMMRATAC or MACS3(which will use theHMMRATACalgorithm forATACanalysis), thenthe best se...
Thanks for developing this function to call peaks for ATAC-Seq. I ranmacs3 hmmratac -i final.bam -n treat --cutoff-analysis-only. Then, I got the report(see the attachment), according to the document, -l may set to45(that can capture moderate number ( about 10k ) of peaks with norm...
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 -f BAM -g hs -n test -B -q 0.01 寻找ChIP-seq的组蛋白(Histone )Mark的命令: ### 生成的文件是broadPeak macs3 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1 对于ATAC-seq双端数据的操作: macs3 callpeak -f BAMP...
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-only ...
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...
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...
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 hmmratac; I use this command macs3 hmmratac -f BAM -i RES/atac/try_1/04-NobiasedRegions...
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...
About ATAC-seq call peak (hmmratac) and differential analysis via MACS3 #676 opened Nov 19, 2024 by DayTimeMouse Q: There's a huge difference between my peak number and the bio company's peak number General Question #673 opened Nov 14, 2024 by bigshark12345 2 Bug: NameError: ...