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• Installing standalone Galaxy with reference geneome
  Dear all, newbie question here.  So I installed Galaxy on my linux box.  When I try to upload a ...
• Editing reference genome for TopHat on Trapline
  I am trying to use the Trapline workflow for RNA-Seq data, and have read the manual. I want to ed...
• Which Reference Genome Should I Select
  Dear All, I am going to run Tophat with mouse RNA-seq datasets. When I uploaded the datasets wit...
• Beginner to Galaxy local installation - tools and reference genomes population?
  Dear all, I'm a very new to a local installation of Galaxy. I have insyalled a local copy by: %...
• Mm9 Reference Gtf File For Cuffcompare
  I wonder if some has mouse genome GTF file compatible with Tophat/ Cuffcompare. The contig names ...
• Problem regarding reference genome
  Hi, I am doing RNA seq. analysis in galaxy (using tophat tool). But problem is that my genome of...
• type of file for reference genome
  i want to use a reference genome for tophat. Which type of file the galaxy will recognize?
• TopHat not working
  My tophat in galaxy is not working. I try to use it to map to the reference human hg19 genome. Bu...
• Genome file for Bam to Bed or Genome Coverage
  I generated BAM (mm9) files in Tophat and tried to convert them to Bedgraphs using the BedTools p...
• Customizing Mm9 Mouse Reference Genome And Then Using That As The Ref Genome When Uploading Illumina Data
  I would like to filter out the mm9 mouse build ref genome to only show MspI sites, and then use t...
• Cufflinks Error With Illumina Igenome .Gtf For Annnotation
  Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcri...
• Concatenate locally cached assembly
  I wish to create a custom build of the mm9 assembly by inserting a FASTA file. Is there a way I ...
• Please Help Me Check The Quality Of The Tophat Mapping To Reference Genome
  Dear All, I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the...
• Inbuilt reference genome
  Hi, I ran a top hat analysis on samples, but after the cuffdiff step, I do not have any genes an...
• Addding iGenomes inGalaxy
  If i download iGenome of particular species (In may case Chicken) from http://ccb.jhu.edu/softwar...
• "View Details" Of Tophat Alignment
  Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters b...
• Reference Genome Format For Tophat
  Dear all, I managed to upload to Galaxy a genome of interest in .fasta format from NCIB website. ...