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• TSS distrubtion for ChIP-Seq
  I have been using ChIP-Seq and want to display peak distribution at the transcription start sites...
• Phastcons score under hi-seq peaks
  Hi, I would like to get the phastcons score (vertebrate first then mammals) under Chip-seq peaks ...
• Visualization of ChIP seq peaks in IGV
  I want to visualize in IGV the ChIP Seq peak form my data but I don't know what file I have to up...
• Displaying Macs Peaks At Ucsc
  Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ ...
• How to do the peak calling with "MACS2 bdgbroadcall" for H3K9me3 ChIP-seq
  Hi, I try to use the MACS2 bdgbroadcall to analyze my H3K9me3 ChIP-seq data, but there is no opti...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• Chip-Seq
  Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one file of input and oth...
• How to find out that Chip-seq peaks falls within promoter or enhancer region of gene?
  Hello, I have got the peaks and their corresponding peak regions from MACS2 peak analysis tools...
• Macs2 Bdgdiff help
  Hello, I am new to processing ChIP seq data I want to do a differential peaks comparison between...
• An odd number of differential peaks in MACS2
  hi, I'm working with ChIP-seq data and using MACS2 version- macs2 2.1.0.20140616. I run MACS2 c...
• ChIP-seq sequence data sources
  hi I predict nucleosome using the chip-seq. i need to chip-seq data (bovine) . please tell me ho...
• 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...
• 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 ...
• Database Of Known Chip-Seq Peaks
  Dear all, please could you recommend any resource/collection/database of known ChIP-seq tracks t...
• MNase ChIP-seq paired-end data analysis ?
  Hello everyone! Sorry for long explanation! I did paired-end ChIP-seq for my input and IP sample...
• update drosophila genome to dm6
  The Drosophila genome has been updated to dm6. However, the Galaxy still only use dm3. Many gene ...
• Annotation Histone Modification ChIP-seq
  Hi there, I am new to this and have used MACS for peak calling and I now want to annotate the pe...
• Macs2 running to one sample
  Good morning, Im working with samples from ChIP-seq, and now i'm using macs2, however when i use...
• Peak Annotation With Galaxy
  Dear Galaxy, I am analysing ChIP-Seq data from Illumina using Galaxy web server. I mapped the re...
• 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...
• How to judge the quantitativity of ChIPSeq?
  Hi, I have now been through my ChIP-Seq analyses with some success using the Galaxy platform up ...
• ChIP seq Motif analysis
  Hi, How to do motif analysis after peak calling? I used MACS2 for peak calling, used fastq to fa...
• ChIP-seq analysis on small genome
  Hello, I am using Galaxy to analyze ChIP-seq data of a mammalian cell line containing virus episo...
• Annotating ChIP seq peaks in Galaxy
  I'm analyzing ChIP seq data using Bowtie and then MACS with the Galaxy web instance, and now want...
• Peak-Calling With Macs From .Bowtie File
  Hi, I have ChIP-seq alignment files in .bowtie format and would like to perform peak-calling usi...