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• Summit Extension in ATAC-seq
  Something I've seen with ATAC-seq analysis is the extension of peak summits (ie. "Peak summits we...
• ATAC-seq peak calling
  Hi Biostars community, I am new to ATAC-seq analysis, hence the following basic questions regard...
• peaks overlap: ATAC & CHIP seq
  Hi guys. I have two peak files. One is from ATAC seq and the other is from H3K27ac chip seq. I am...
• Low number of peaks and weird TSS profile
  Hi, I am looking at ATAC-seq data of good/decent quality. I used MACS2 for peak calling and was ...
• Differential Peak Expression in ATAC-seq data
  I was wondering if anyone had experience dealing with determining statistically significant peaks...
• MACS2 option for ATAC seq?
  I have some ``ATAC-seq PE`` samples and `Dnase-seq SE` samples, I like to do peak calling for th...
• shift direction in ATAC/DNase data?
  I have two set of data about ATAC-seq and DNase-seq and I like to perform peak calling using MACS...
• macs2 call peak
  I used macs2 to call peaks for chip-seq data.But I do not know why macs2 will slide two bandwidth...
• How do I select top 100,000 non-overlapping peaks from MACS2 narrow peaks output?
  Hello everyone, I've just finished MACS2 narrow peak calling ATAC-seq data. With a cut-off q-val...
• Best practice for analysing ATAC-seq data
  I am trying to analyze some ATAC seq data. I performed paired-end sequencing on six samples. Thre...
• How to compare peaks (called by MACS2) within a specific genomic area for two samples?
  Hello, I have two ATAC-Seq peak samples for the same subject. I want to quantify the ATAC-Seq pe...
• Normalizing ChIP-seq and ATAC-seq data?
  I have some Single end and Paired end ChIP-seq and ATAC-seq data. I have done aligning using Bowt...
• macs2 callpeaks genome
  Hi guys, I have a question about MACS2 to call peaks from either chip-sew or ATAC seq. When I use...
• Fseq versus MACS2 for ATAC-seq
  I wish to compare two biological conditions with respect to their open chromatin. I use ATAC-seq ...
• Normalization and differential analysis in ATAC-seq data
  Hello everyone! I would like to know if someone had experiences with normalization and different...
• How does MACS algorithm work on ATAC-seq data if there is no control sample and no model estimation?
  I understand that unlike for ChIP-seq, with ATAC-seq MACS doesn't estimate the model, which means...
• Peak call? or Just convert to bedfile by bedtools bamtobed? to generate the accessibility matrix of single-end single cell ATAC-seq
  I'm wondering about the "single-end" single cell ATAC-seq (scATAC-seq) analysis. The reads obtain...
• Where are the actual transcription factor binding sites located in the CHIP-seq peaks
  The peaks of a particular Transcription factor CHIP-seq as identified by multiple peak calling al...
• comparing ATAC-seq/ChIP-seq peaks
  We want to do a meta-analysis on previously analyzed ATAC-seq data from different cell types. It ...
• Macs2: predicted fragment length less than 2*tag length
  I am using macs2 2.1.1.20160309 to call peaks on narrow peak ChIP-Seq data set that is sequenc...
• ATAC-seq peak calling?
  I have some PE ATAC-seq data and i like to do peak calling using MACS2. I found that If I like u...