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• Error Message
  Hi- I'm trying to filter the data from 3-way RP scores on the UCSC browser before importing into...
• Problem With Downloading
  Hi I am trying to download the results of my analysis (.sam files) from Galaxy main. The downloa...
• Problem with toolshed installed deepTools on CloudMan instance
  I successfully installed deepTools using the toolShed from the Galaxy main repos. The problem is ...
• Cufflinks Output In Ucsc Browser
  Hi all, I am doing cufflinks assembly of TopHat-aligned NGS reads with Refseq gene track as refe...
• Bad Value For -Sequence With -Auto Defined
  I have been importing fasta files into galaxy then attempting to GetOrf on these files.  I have b...
• Filter Crash
  Hi! I use galaxy 2.2 I extract all snps from snp125 (whole genome, hg17, i use ucsc browser mai...
• Error in local Galaxy's "display at UCSC main" command
  Hi all I have a BAM file uploaded I want it to be visualize over at UCSC Genome Browser through ...
• What is causing this MPileup error in Galaxy?
  Hello, I'm new to galaxy and next gen sequencing.  I'm trying to generate a VCF file from whole ...
• Main galaxy instance not working
  I am a user of the main Galaxy server, and, this morning, I cannot get any tool working, when I c...
• [Genome] Genome-Wide Dataset Of Protein Location Conversion
  Hi Dana, the way I do it, is the following: Get a list of all genes (e.g. RefSeq) using the "Ge...
• Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'
  Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to gen...
• Using Ensembl gene annotation with Galaxy
  I'm trying to use ensembl gene annotations for my tool* but I don't understand how to map them to...
• Error Message with Galaxy Main Diffbind
  I know a similar problem has been posted before, but I could not comment on the original post: I...
• Can you use Galaxy Lift-over to convert ce10 genome coordinates to ce11?
  I am trying to convert wig (or bigwig) and bed (or bigbed) files from the UCSC ce11 (WBcel235) co...
• MACS2 bdgdiff output empty
  hello, I'd like to report an issue I've been having with the MACS2 bdgdiff function in the Galax...
• Conservation (I.E. Phastcons) Q
  Hi All, I am using Galaxy (main) and would like to intersect a bed file I have with the PhastCon...
• Upload/Other tools at Galaxy Main https://usegalaxy.org producing errors -- Resolved, review for details
  What is Internal Server Error (500)? I am using Galaxy Main (usegalaxy.org). About 1 to 1.5 hou...
• Basic Genome Loading Question
  Hi everyone, We are running a local version of galaxy off of our server. What is the best way to...
• Error with "Trim leading or trailing characters" tool
  Hi all, I have been trying to trim my fastq files, and I am running into problems. I used the "T...
• Tophat Problem On A New Local Instance
  I have installed a local instance of Galaxy as a one user in a Mac Pro desktop. I got some valua...
• Deeptools module in galaxy main instance
  This is a follow-up from a previous question. The Deeptools module in the main instance of gala...