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• MACS2 bdgdiff output empty
  hello, I'd like to report an issue I've been having with the MACS2 bdgdiff function in the Galax...
• 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 ...
• Compare bedgraphs of two treatments after MACS2 callpeak.. do I need SPMR?
  Hey y'all, I'd appreciate your help here! Do I really need to use the SPMR option in MACS2 to co...
• Bam to Bedgraph error
  Hello, I am trying to convert bam files to bedgraph files and eventually to bigwig to visualise ...
• Color in a bedgraph / bigwig
  Hi all, I'm doing ChIPseq with the galaxy main server using Bowtie2 & MACS2. I then transfor...
• 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...
• Output Files of MACS2 bdgdiff
  Hello everyone, I have some bedgraph files from a ChIP-Seq experiment (2 replicates for each cond...
• MACS and BDGdiff
  Hi, I run MACS2 with broad and paired-end settings, but it did not produced any lambda files whi...
• Convert BAM into bigwig for chicken
  Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to-bigWig” in G...
• Genome Coverage without hg19 reference genome
  Hi, I have human hg19 RNA-Seq bam files, and would like to use Genome Coverage to convert bam to...
• MACS2 bdgdiff output is empty
  Hello, I'd like to report an issue I've been having with the MACS2 bdgdiff function in the Galax...
• Macs2 Bdgdiff help
  Hello, I am new to processing ChIP seq data I want to do a differential peaks comparison between...
• Bedgraph column 1
  I used Bedtools to generate Bedgraphs from Bam files. Column 1 only contains a number that is not...
• Wig/BedGraph-to-bigWig fails with "hashMustFindVal: '1' not found Error running wigToBigWig."
  Hi, I have a very large, merged BAM file which I successfully converted to a bedgraph using the ...
• Chrom len file bedgraph to bigwig
  What is the best tool to use or where can .len files be found for the bedgraph to bigwig tool. I ...
• How to do differential peak analysis after scaling bam files?
  Dear all, I am trying to analyze my spiked-in ChIP-Seq data by scaling my original aligned BAM f...
• Error of wig/BedGraph-to-bigWig converter
  Hi, I have a ChIP-Seq BAM file aligned on the chicken galGal3 reference genome using Bowtie2. I ...
• Bedgraph file problem
  I have received a set of BAM files generated from RNAseq (PE100) of the opossum, MonDom5. When ...
• Need help with "Create a BedGraph of genome coverage" tool
  Hi there I am trying to calculate the coverage of my alignment based on the BAM file using "Crea...
• Genome file for Bam to Bed or Genome Coverage
  I generated BAM (mm9) files in Tophat and tried to convert them to Bedgraphs using the BedTools p...
• ChiP Seq Track height and scaling in UCSC Browser
  Hi all, I recently work on several ChIP-seq data sets. My traditional workflow is .fastq/.fastq....
• 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...