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• Intersection of replicates
  I have a question regarding a tool of Galaxy. I have done the Peak Calling of all my 12 samples ...
• Help
  Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommende...
• (No Subject)
  Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommende...
• Chip Seq analysis with multiple biological replicates for differential expression
  Hello, I am very new to sequence data analysis and had some structural questions. I am trying to ...
• Diffbind and repmatch fatal error
  Hi! I have 3 chip replicates and I want to find common peaks within them. I used diffbind to do s...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• Incorporating biological replicates to identify statistically significant changes between two different "treatment" samples and one "control" in ChIP-Seq
  I performed a ChIP-seq experiment in which I'm looking at H3K4me3 levels under three conditions. ...
• calling peaks without control
  Hi again! I was wondering, when I call peaks with MACS using my treatment and control, I get 1600...
• INTERSECT Genomic Intervals returns empty files
  Hi, somehow the Operate On Genomic Intervals - Intersect the intervals of two data sets doesn't ...
• Irreproducible discovery rate (IDR)
  Hello, I was trying to measure the reproducibility of the 3 set of peaks identified from three r...
• Unable To Run Sicer Or Find Peaks
  Hi, I want to use SICER or Find Peaks for peak calling on GALAXY. I am using my aligned ChIP-se...
• genome mappability and peak calling
  I am working with a brassica plant that it is not the model Arabidopsis thaliana. How important i...
• peaking calling in MACS shows error?
  Hi everyone im trying to do peak calling using MACS in Galaxy(default settings) for dataset SRX6...
• peak calling in MACS2
  I am trying to do peak calling of paired-end sequences using MACS2 in Galaxy. The Filter SAM file...
• Peak Calling on BED files
  This is somewhat of a naive question. I've been using MACS2 on galaxy to call peaks on my ChIP-s...
• ChIP seq Motif analysis
  Hi, How to do motif analysis after peak calling? I used MACS2 for peak calling, used fastq to fa...
• IDR with Mm10
  Hi, I am interested in comparing peaks from replicates using IDR. I have found that this [Galaxy...
• Output Files of MACS2 bdgdiff
  Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each cond...
• Problems with MACS peak calling--FDRs of 100%
  Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (in...
• Find Common Peaks between two independent samples
  I was wondering if there was a function in galaxy where if I input two (or more) Bed files where ...
• Macs- Duplicate Reads Removal
  Hi, Does MACS remove duplicate reads automatically during the peak calling? I'm running controls...