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• Problem with toolshed installed deepTools on CloudMan instance
  I successfully installed deepTools using the toolShed from the Galaxy main repos. The problem is ...
• multiBigwigSummary doesn't work with me
  Hi all, I tried to use multiBigwigSummary in DeepTools in Galaxy, but i always got this message:...
• Deeptools compute matrix
  I love Deeptools, and so glad that galaxy has moved them to the main server. It's awesome! I can...
• Wig To Bigwig Error
  Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each...
• (No Subject)
  Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each...
• Tool errors with private instance of Galaxy on Jetstream
  Hello community, I manage a NGS core lab and also teach a grad level intro to Bioinformatics cou...
• problem with megablast
  Dear,   every time I recently tried to do a Megablast search, I get the following error: File...
• Error message: "The number of labels does not match the number of BAM files", when running bamCoverage
  Hi Running plotCoverage (Deeptools) on a single (or multiple) filtered BAM file(s) returns a com...
• DeepTools plot correlation image error
  Hi guys, I am trying to make some nice images out of my ChIP-seq data. I want to compare regions...
• 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?   ...
• Trouble sorting a BAM file
  Hi I have aligned reads to Brassica juncea genome 1.5 using HISAT2. Now i want to perform PCA an...
• Problem with custom tool that uses bioperl modules in local Galaxy instance
  Hello, I am writing custom tool for Galaxy that uses perl scripts and bioperl modules. My instan...
• TypeError while executing sh run.sh
  I am trying to run my galaxy instance off of a remote server and when I execute sh run.sh, I get ...
• Failure to import a file from a history, in Galaxy Test
  A coworker shared a file with me in a history on Galaxy Test, so that I could explore the deepToo...
• computeMatrix not working
  Hi, I keep getting this error: Traceback (most recent call last): File "/galaxy-repl/main/jobd...
• MACS fails, finds peaks but can't build model
  Hi,  I'm using the Galaxy GVL-QLD instance.    I have single reads chip-seq files from E. coli...
• Wig/BedGraph-to-bigwig converter doesn't recognize my bedGraph file - why?
  Hi, Am new to Galaxy but has successfully converted a number of downloaded Wig files to bigWig f...
• deepTools2: compute matrix error
  I get this error when trying to use computeMatrix in the DeepTools2 suite: Fatal error: Exit...
• Cufflinks Failure Error - Solution: use version 2.2.1.2 or later
  Hello, I've been trying to run cufflinks on my bam files for the last couple of house and keep ...
• 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/...