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• No Zebrafish Danio Rerio Reference genome in Tophat2 drop down
  No Zebrafish Danio Rerio Reference genome in Tophat2 drop down Please advise. Many thanks
• Please add the zebrafish genome to tophat
  Can you add the latest zebrafish genome danio_rerio_zv10 to the tophat reference genome? Thank yo...
• zebrafish genome for HISAT
  Hi, Any way to get the zebrafish genome added to the HISAT package? either zv9 or zv10? Thanks! Rich
• Arabidopsis genome to HiSat2
  Would it be possible to get the Arabidopsis thaliana genome pre-loaded into HISAT2 on Galaxy Main...
• 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...
• Missing genome in Tophat2
  Hi Galaxy Team, Is there any way to get the latest Zebrafish (Danio rerio) genome added to the r...
• HISAT2 reference genome unobtainable
  Trying to use HISAT2 - no reference genomes are available, how should I report this? Many thanks,...
• No reference genomes on galaxy hisat2
  I am trying to do rnaseq analysis but galaxy doesn't seem to have any reference genomes on hisat2...
• Add reference genome
  Hi, Is it possible to add Arabdiopsis as reference genome to the build in set for the hisat2 pro...
• HiSat2- over 50% of reads failed to align
  Hello, I am using Hisat2 to align reads to a reference genome (mm10). However, over 50% of read...
• unable to load zebrafish GTF/GFF3 files from current history into any of the RNA analysis tools
  I am analyzing zebrafish RNA seq data, I am able to upload the fastq files, use trimmomatic, alig...
• 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...
• HiSAT2 alignment to GRCm38? in Galaxy -- where to find mm10 reference annotation
  I am doing an RNA-seq experiment and I ran HiSAT2 with the mm10 reference genome. Then in order t...
• HISAT2-reference genome not available in a local -- data must be installed first
  Hi everyone, When I'm trying to use in my local galaxy HISAT2 for mapping the reads I have an inf...
• Which reference to map against for RNA-Seq using HISAT2
  Hi all, I am trying to determine differential expression between two test conditions - in rat. T...
• Problems loading/using custom genome dataset for Hisat analysis
  Hi, I am trying to load from ENA the genome dataset of Carnegiea gigantea into HiSAT2 analysis f...
• Cufflinks output file with many 0 FPKM values
  Hi, I have run Cufflinks on my zebrafish RNAseq reads mapped using Tophat2. The Cufflinks output...
• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...
• 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...
• Uploading Genome From Ensembl
  How do I upload the Zebrafish genome from Ensembl to my user history in Galaxy? I'm trying to map...