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• DiffBind differential binding analysis of ChIP-Seq peak data
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• Sorting ChIP-Seq peaks
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• Overlapping/Intersecting Tracks in IGV
  Hello How can i Overlapping/Intersecting Tracks in IGV. I have 2 peaks in seperat...
• Genome name in Bam file, IGV visualization problem
  I am using IGV for Mac (2.3.68) to visualize the alignments I made in Galaxy against E.coli MG165...
• 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 ...
• RNA seq peaks
  how to visualize RNA seq peaks (what format) between different conditions in UCSC genome browser....
• Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
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• 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...
• Macs2 Bdgdiff help
  Hello, I am new to processing ChIP seq data I want to do a differential peaks comparison between...
• Exon, Intron or Promoter?
  Hello, I need help you. I have a file of CHIP-SEQ data in BED format and i analyzed those data wi...
• Track visualization tool
  Hello, I haven't been able to visualize my ChIP-Seq peaks using track visualization tools. Previo...
• Displaying Macs Peaks At Ucsc
  Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ ...
• Annotation Histone Modification ChIP-seq
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• Filter Wig file
  I would like to filter a wig file from a ChIPSeq Peak calling program by its control ChIPSeq Peak...
• Weird Peak calling results
  Hi Everyone, I need help with Galaxy-Macs' Peak Calling tool. Using my ChIP-Seq data (Experimen...
• 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...
• 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
  Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one file of input and oth...
• MACS2 input not recognized by tool
  Hi all, I've been using Galaxy to analyze my ChIP-seq data, and have managed to get the program ...
• 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...
• 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...
• computeMatrix with bed
  Hi, I am using the CLC genomic workbench to analyze my ChIP-seq samples- would like to use Galax...
• Is There Any Way To Calculate % At Or Gc Of A Group Of Sequences?
  I am looking at a file of peaks from ChIP-chip data and would like to know whether there is a way...
• Analyzing ChIP-seq data from HiSeq 3000
  I have acquired ChIP-seq data from an Illumina HiSeq 3000. I have followed the analysis workflow ...
• no bam visualization into IGV
  Hi all, I've done a tophat2 mapping of human RNA-seq expts in usegalaxy.org. After getting the a...