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• Missing genome in Tophat2
  Hi Galaxy Team, Is there any way to get the latest Zebrafish (Danio rerio) genome added to the r...
• TopHat Reference Genomes: Where has the zebrafish reference genome gone?
  Hello Galaxy Team, I'm still a little new at using Galaxy, so please bear with me if this is a s...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• Zebrafish Genome on HISAT2
  Hello, The reference genome for zebrafish (D. Rerio) is missing from Hisat2. Could this be added...
• Please add the zebrafish genome to tophat
  Can you add the latest zebrafish genome danio_rerio_zv10 to the tophat reference genome? Thank yo...
• FastQC form setting and usage
  What does Contaminant list mean? For an example when I select the settings for the FastQC:Read QC...
• Tophat can't see the build-in reference genome?
  I successfully fetch an hg19 and build an bowtie2 index with Data managers. Bowtie2 can see the r...
• Adding Danrer7 As A Reference Genome For Tophat2
  Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat fo...
• Reference genome absent
  Dear Biostar, For mapping our paired end reads against horse, we are unable to find a reference ...
• built-in genome for HISAT2 not available
  I am trying to map fastq to mm9 genome using HISAT2. But the drop-down list of built-in genomes i...
• Help
  Hello; I am having the following problems with RNAseq using galaxy; we have installed the Galaxy...
• Custom genome for galaxy- Ensembl reference genome
  I want to perform a DEXseq analysis on alternative splicing, and it requires to map the RNA-seq d...
• BWA-MEM Tool not recognizing fastq inputs
  I am attempting to use the NGS mapping tool BWA-mem. I have uploaded my reference genome, in addi...
• Large Transfer Between Cloudman Instances
  Hi I've got 2 clusters running TopHat2 for several large data sets in Cloudman. In one, the olde...
• STAR --> option for reference genome
  Hi, I have been trying to test RNA-Star on the Galaxy main server, but in the option for 'Select...
• Genome Not Available On Galaxy
  Hello, I am a new galaxy user and cannot find my reference genome in the drop down menu. I perfor...
• Galaxy Not Showing My Reference Genome In Drop Down For Bowtie
  Hi guys, As shown in the attached screenshot I uploaded a fasta file. And I want to use it as m...
• Adding reference genomes to local instance of Galaxy using Rsync
  Hi everyone, We were finally successful in downloading selected reference genomes as they appear...
• Adding Reference Genome
  Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in gala...
• 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 ...