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• Problem with custom reference genome
  Dear all, on our local galaxy-docker-stable instance I would like to include additional referenc...
• tophat reference genome
  Kindly add the genome of Pinus taeda and Picea glauca to the tophat reference genome as I am unab...
• Problems In Transitioning From Tophat To Cuffdiff
  After successfully using RNAseq software in Galaxy online for about 10 different datasets to jus...
• Error message in Tophat
  I am receiving the message "an error occurred setting the metadata for this dataset" on all jobs ...
• Galaxy Local Install Problems Understanding Where To Put Mouse Ref Seq Data To Populate Ref Genome In Bwa
  Hello, I am still having problems understanding how to install mm9 mouse ref genome into our own...
• Problem with TopHat in Galaxy using data from Nature Protocols
  Hi, I am a graduate student who began RNA-seq data analysis recently. I am having a trouble with...
• TopHat from Galaxy local instance do not recognize available fastq files.
  Hi there, I am probably missing something obvious here. My local Galaxy TopHat does not recogniz...
• Trackster Not Showing Visulization
  Hello, I am trying to use trackster to compare samples against a reference genome. I have upload...
• Saccharomyces cerevisiae reference genome for TopHat,Bowtie
  Hi, I am new to Galaxy, and for my first project I wish to analyze some sequences we recently ob...
• gtf file error
  Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fast...
• Reference Genome Format For Tophat
  Dear all, I managed to upload to Galaxy a genome of interest in .fasta format from NCIB website. ...
• Problems With Tophat
  Hello, I have successfully used the public server for processing RNAseq data but I have run into...
• Local Tophat Error "OSError: [Errno 2] No such file or directory"
  I have created a local Galaxy server to run RNA analysis. I am trying to run TOPHAT on a fastasa...
• Running TopHat2 with a GTF file
  Hi everyone,   I am having issues running TopHat 2. I have added the reference genome fasta fil...
• BWA for Illumina using custom genome
  Hi I have uploaded the fasta files (3 chromosomes) of my genome of interest. I downloaded FASTA ...
• CuffDiff error, "Uncaught exception in exposed API method," job runs, but no results
  Hello, I’ve run into a problem while analyzing some RNAseq data on usegalaxy.com. I am looking...