Similar posts • Search »

• Summit Extension in ATAC-seq
  Something I've seen with ATAC-seq analysis is the extension of peak summits (ie. "Peak summits we...
• 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...
• 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...
• 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...
• 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...
• macs2 callpeaks genome
  Hi guys, I have a question about MACS2 to call peaks from either chip-sew or ATAC seq. When I use...
• 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...
• Normalization and differential analysis in ATAC-seq data
  Hello everyone! I would like to know if someone had experiences with normalization and different...
• Fseq versus MACS2 for ATAC-seq
  I wish to compare two biological conditions with respect to their open chromatin. I use ATAC-seq ...
• 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...
• comparing ATAC-seq/ChIP-seq peaks
  We want to do a meta-analysis on previously analyzed ATAC-seq data from different cell types. It ...
• 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...
• 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...
• MACS2 gives negative estimated fragment length
  Hi, I have two ChIP-seq replicates and their peak profile looks very similar in genome browser. ...
• Calling differential peaks on ATAC-seq data
  My lab has recently run an ATAC-seq analysis on 3 biological conditions (Day 0, day 1 and day 7) ...
• How does MACS2 assign pValue? and how does changing the cutoff effect results?
  I'm curious as to how MACS2 assigns a p-value due to the following problem I'm having right now. ...
• How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K4me1)?
  I have a set of ATAC-peaks which I would like to correlate, somehow, with the level of H3K4me1 fl...