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• Bam to BigWig conversion fail
  I tried converting my sorted bam files to bigwig (my build is mm10) and got this error: 1 is ...
• Bam file can not convert into bigwig
  Hello, I got a bam file and upload to the Galaxy.  When I convert it into bigwig, it gives me th...
• BAM to FPKM bigwig file
  Hi, I am new to RNA seq analysis.I am wondering if some one help me with the conversion of .BAM ...
• Convert Sam To Bigwig
  Hi, What is the 'official' method of converting a BAM file to a bigwig on the public server? I ...
• Convert BAM into bigwig for chicken
  Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to-bigWig” in G...
• Recent problems writing Bigwig from Bam files
  I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A ...
• Sam To Bigbed
  Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It lo...
• File Uploads
  I am trying to upload .bam and .bigwig datasets, from geo, into galaxy. Galaxy will not recognize...
• Displaying bam or bigwig files in UCSD genome browser
  Hello, I am attempting to view my RNAseq mapping file output (SAM) on the UCSC genome browser. T...
• Bam to Bedgraph error
  Hello, I am trying to convert bam files to bedgraph files and eventually to bigwig to visualise ...
• 'Sampling' Bam or BigWig files?
  I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. N...
• Bam To Bigwig
  Hello, I am trying to convert a BAM file to Bigwig using the Convert Format option under Attribu...
• Bigwig to Wig or Bgr
  How can I convert a Bigwig file to Wig or Bgr? Is there a utility on Galaxy that can do this?   ...
• 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 ...
• Picard 'CollectRnaSeqMetrics' run on hg19 Tophat BAM in Galaxy yields no exonic reads, all intergenic
  Greetings, I am trying to obtain basic alignment metrics for human 50bp-paired end RNA-seq fil...
• filtering pair-end bam file
  Hello, I am trying to filter a pairend bam file to get only forward reads in Galaxy. A bam filter...
• 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 ...
• Visualizing BigWig is UCSC genome browser: link not available
  I wish to visualize some bigwig files generated from bamCoverage tools in the UCSC genome browser...
• 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...