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• Exon, Intron or Promoter?
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• Peak Annotation With Galaxy
  Dear Galaxy, I am analysing ChIP-Seq data from Illumina using Galaxy web server. I mapped the re...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• 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...
• Motif discovery-Chip seq
  Hello, I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads wi...
• Fetching Promoters
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• Tophat Mapping
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• Output Files of MACS2 bdgdiff
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• How to determine genome wide Co-occupancy between two transcription factors? by Galaxy main
  Hello: I am currently using Galaxy to analyze several sets of ChIP-Seq datas, including those pu...
• ChIP-seq workflow help
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• Chip-Seq Data Analysis Question
  Hello, My name is Christopher Terranova and am a M.S student at the University of Buffalo SUNY.I...
• Get fasta file from peak called BED file to do Motif analysis
  Hi all, I have some called peaks in BED format and would like to extract the sequences in a FAST...
• normalisation between different ChIP-seq data
  Hi there, I guess it is a recurrent problem, but I haven't found a satisfying answer yet. I have ...
• update drosophila genome to dm6
  The Drosophila genome has been updated to dm6. However, the Galaxy still only use dm3. Many gene ...
• Galaxy: Genomic Intervals to strict BED Conversion
  Hello: I'm new to the forum and Galaxy/bioinformatics. In the last two months I've been followi...
• 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...
• Need help with "MACS" tool
  Hi everyone, I don't quite understand the meaning of the parameters of this program.  1. What i...
• Filtering list of regions to known refseq areas
  Hi, I have a set of Chip-seq-like data aligned to mm9, and have run SICER to peak call, thus gene...
• How to calculate differential methylated regions from MeDIP-seq data in Galaxy
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