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• 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...
• 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...
• 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...
• model based analysis of chip sequencing
  what is the meaning of forward tags and reverse tags in peak model of Model based analysis of chi...
• WIG file from MACS2
  Hi, I have been using MACS2 in Cistrome to call peaks from ChIP-seq data. It appears as though i...
• TSS distrubtion for ChIP-Seq
  I have been using ChIP-Seq and want to display peak distribution at the transcription start sites...
• Database Of Known Chip-Seq Peaks
  Dear all, please could you recommend any resource/collection/database of known ChIP-seq tracks t...
• 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...
• Chip Seq analysis with multiple biological replicates for differential expression
  Hello, I am very new to sequence data analysis and had some structural questions. I am trying to ...
• 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...
• 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 ...
• Displaying Macs Peaks At Ucsc
  Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ ...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• 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...
• 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...
• Different results with manual MACS tool vs. workflow automated MACS tool for ChIP analysis
  hi, i wanted to post about something i found out today working with the MACS tool (under NGS: pe...
• 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...
• Chip-Seq
  Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one file of input and oth...