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• Identifying differential histone mark (H3k27me3 and H3k4me3) in treated and control sample
  Hi,, I'm analysing chip seq data for histone mark h3k27me3 and h3k4me3. for each condition, I ha...
• Analyzing genome wide sequencing data for control and experimental groups with biological replicates.
  Hello, I am very new to sequence data analysis and had some structural questions. I am trying to ...
• Peak Calling Biasing!!! [Macs14]
  Hi guys, I got puzzled by the peaks called by MACS14 peak caller. Attached is the image where bl...
• Comparing numbers of ChIP-seq peaks between different sample types
  Hi everyone, I have a bit of an odd question which admittedly has come more from my PI than me. ...
• How to deal with low-depth ChIP-seq / ATAC-seq samples
  Hi all! I got several ATAC-seq and ChIP-seq samples, but unfortunately, some of them are with lo...
• ChIP-Seq Histone modification time span study
  I am analysing ChIP-seq data for histone protein. The study is timeline study. It aims to study ...
• Identifying novel ChIP-seq peaks in KO samples compared to WT
  I have two ChIP-seq tracks of a histone modification from WT and KO cells which have been process...
• Paired-end ChIP-Seq Peak Calling
  Hi, I have some CHiP-Seq data for transcription factor binding in Arabidopsis Thaliana (the mode...
• 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...
• Large Number Of Macs Negative Peaks
  I have a TF chip-seq study with two types of replicates: 2 Flag+TF samples, each with a corresp...
• For Chip-seq, which control data I should choose for each biological replicate samples in MACS2
  I have control and experimental groups, each has 3 biological replicates. When I do the Call pe...
• Combining the original replicates and pseudo-replicates for differential binding analysis?
  Hi. I want to compare the differential binding of suz12 (mixed peaks) in two conditions; Control...
• Finding common peaks between F-seq peak region files
  I have 3 biological ATAC-seq conditions, each with two replicates. I have obtained F-seq region...
• How to compare different chipseq peak calling methods?
  Hi, I have been using various peak calling methods like MACS2, JAMM, BinQuasi and Zerone across t...
• Chip-Seq Peak Calling Using Macs In Galaxy- Overlapping Peaks For Replicates
  I have two replicates from one cell type (chip-seq data). I aligned each one in galaxy using bwa....
• how to find differential region between my replicates.
  Hello , I did chip experiment with three replicates for two conditions ( normal condition(C) and ...
• Comparison of replicates from NGS : merge before or after peak calling ?
  Hello everyone !! I have a question for you : I have biological replicates from Atac-seq experi...
• MACS2 Peak Calling : Different number of peaks for each replicate
  Hi All, I am a newbie and I am doing a ChIP-Seq analysis on a small dataset of 6 samples (Wild-t...
• Chip-Seq (IP-vs-Control and Mock-vs-Control) or IP-vs-Mock for peak calling
  Dear All, I would be really grateful for your advice in this regard. In Chip-Seq where there are...
• MACS/MACS2 Peak calling failure with Paired End ChIP-seq data of 125bp read length
  I have a TF ChIP-seq time course study with read length of 125bp Paired end around 30 to 50M pair...