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• Trouble using interval2maf.py
  Hello, I have installed a copy of the main Galaxy distribution onto my local system - and am cur...
• Galaxy fail to share history with a single user
  Hi, I am running the latest galaxy (latest_15.05) and I noticed that when I try to share a histo...
• RNA-STAR Failing using hg38 but works for hg19
  Hi, I am trying to align two collections of 4 single-end RNA-Seq fastq files (8 fastq files tota...
• HTSEQ count error
  Hello, This is my first rna-seq data analysis project and I am using Galaxy to analyze different...
• htseq-count failed with error no exon found
  I am having trouble with htseq-count. My gff file i.e. [brassica juncea .gff file][1] does not co...
• Cuffcompare successful but generate empty files.
  Hello friends I am currently doing RNA-seq for 3 datasets (obtained publicly through NCBI-SRA...
• Question About Unified Genotyper
  I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are ...
• Problems with Bamtools: Filter BAM
  Hi, I seem to have a problem with filtering merged BAM files following a recent update. I am tr...
• MACS2 not working on bam files - possible error with alignment?
  Hi all, I have successfully called peaks on my bam files using earlier versions of MACS, however...
• Bam To Bigwig
  Hello, I am trying to convert a BAM file to Bigwig using the Convert Format option under Attribu...
• clip adapter sequences
  Hello, I am trying to clip adapter sequences from fastq files, however when I open this tool it ...
• 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...
• Cufflinks Gene Transcripts
  Hi I have been experimenting with Bowtie and Cufflinks and I now reach a point where it appears t...
• FTP transfer problems
  Hello, I am trying to upload some files through FTP, I am having this error that I do not know ho...
• Built-in indexes not working in Local Galaxy Instance
  Hi, I've just finished setting up a local Galaxy instance and everything works fine except for b...
• Error: htseq-count exceeds memory buffer, Solution: Set sort option on tool form to Yes
  Hello, I am dealing with RNA-seq data and I was successfully able to align my raw FASTQ data to t...
• Filezilla FTP fails with error "ECONNREFUSED - Connection refused by server"
  Hi Everybody, I am unable to upload my files using FileZila FTP client on Galaxy.... The error ...
• Subtract
  Hello, I am using the subtract (whole dataset) tool. I converted my fastq file to tabular with 2...
• 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...
• Equicktandem Search Not Yielding Any Results
  Hello all, I am certainly new to using galaxy and I have already checked the message boards to g...
• Variant analysis using Galaxy - tutorials, example workflows
  I have my FASTQ files, and I am trying to align them to the mouse reference genome, and perform v...
• ODoSE not working properly. Does an ODoSE manual exist?
  I am struggling with ODoSE since a while with no success. I cannot find a way so use the select ...