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• 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...
• 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...
• Displaying Macs Peaks At Ucsc
  Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ ...
• Sorting ChIP-Seq peaks
  Once I have ChIP-Seq peaks from MACS, I am wondering if there is an easy to sort the peaks accord...
• ChIP-seq workflow help
  Hello, I am a rookie of processing ChIP-seq data, I get a dataset which is about neuroblastoma. ...
• MACS fails, finds peaks but can't build model
  Hi,  I'm using the Galaxy GVL-QLD instance.    I have single reads chip-seq files from E. coli...
• Chip-Seq, Encode Peaks And Galaxy
  Hi everyone, I have a list of genomic regions with some variants and would like to study the cor...
• SICER and mm10
  Hi, I am trying to analyze my chip-seq for Histon modifications by the use of SICER. Once I selec...
• MACs Peak Calling Zero Division Error
  I am trying to use IGB for ChIP-Seq analyses and comparisons.  I am starting with fastq files.  I...
• Help! Galaxy MACS Peak Calling-
  Hi I have aligned my ChIP-Seq and Input to genome and created SAM files. I tried to do peak call...
• 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...
• ChIP-seq analysis on small genome
  Hello, I am using Galaxy to analyze ChIP-seq data of a mammalian cell line containing virus episo...
• Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
  I am planning to use exogenous chromatin as a spike in control with my actual sample from mouse t...
• Peak Annotation With Galaxy
  Dear Galaxy, I am analysing ChIP-Seq data from Illumina using Galaxy web server. I mapped the re...
• Phastcons score under hi-seq peaks
  Hi, I would like to get the phastcons score (vertebrate first then mammals) under Chip-seq peaks ...
• MACS gives the same output using different inputs and with no input
  Hi, we use MACS to call peaks for all of our ChIP-seq data and it has never given us any problems...
• 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...
• MACS error while analyzing ChIP-seq peakes
  Hi, I am analyzing my ChIP-seq data. I am pretty sure I am following the workflow correctly, beca...
• Chip-Seq S.Cerevisiae Ion-Torrent
  Hi everybody. I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak Calling/MACS. I ha...
• Post Galaxy-Chip-Seq Analysis: Ucsc Genome Browser Can'T Read The Wig File
  Hello, I am using the Galaxy web tool to analyze ChIP-seq data. By applying MACS algorithm, the ...
• MACS2 bdgdiff gives empty results in galaxy, what to do?
  Hi all, I am trying to generate differential peaks of 2 sets of ChIP-seq experiments: cells trea...
• Help with Chip-Seq data analysis without input!
  Hi! I am new in galaxy and I am trying to analyse the sequences of a ChIP-Seq.I have been reading...
• A Question in ChIP-seq Normalization
  Excuse me? A few days ago I read a paper "Histone modification levels are predictive for gene exp...