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• bam to stranded bigwig?
  Hi, I have a bam file generated from stranded RNA-seq data - is it possible to use galaxy to spli...
• Recent problems writing Bigwig from Bam files
  I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A ...
• 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 Bigwig
  Hello, I am trying to convert a BAM file to Bigwig using the Convert Format option under Attribu...
• 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...
• 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...
• Sam To Bigbed
  Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It lo...
• visulizion of peak from bamcomparei n UCSC
  I am using bamcompare in Galaxy for the first time to normalize the bam file of my chip.seq data....
• bed file to bigwig file conversion
  Hello there, I want to convert my bed files to bigwig files in order to visualize them using IGV...
• File Uploads
  I am trying to upload .bam and .bigwig datasets, from geo, into galaxy. Galaxy will not recognize...
• 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....
• Creating Trackhub and uploading data from Galaxy to CyVerse
  Hi, I want to create a trackhub for displaying all my data in UCSC Genome Browser. As suggested ...
• 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...
• Viewing BIGWIG files in UCSC
  Hello, Previously I have been able to view BigWig files by clicking on the job, and selecting Di...
• Deeptools module in galaxy main instance
  This is a follow-up from a previous question. The Deeptools module in the main instance of gala...
• 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?   ...
• How to add a custom color to BigWig files
  My wig files are too large for visualization in the UCSC browser.  I used the Galaxy utility Wig/...