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• 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...
• Cuffdiff Question About Using An Unspecified (?) Database/Build
  Hello! I have an RNA-Seq project which consists of 5 samples from the species tr...
• 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...
• 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...
• FastQC form setting and usage
  What does Contaminant list mean? For an example when I select the settings for the FastQC:Read QC...
• No Zebrafish Danio Rerio Reference genome in Tophat2 drop down
  No Zebrafish Danio Rerio Reference genome in Tophat2 drop down Please advise. Many thanks
• Problem With Gatk Tools Not Accepting Bam File As Input
  I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whol...
• Reference genome absent
  Dear Biostar, For mapping our paired end reads against horse, we are unable to find a reference ...
• Display a file stored in database
  hii I am integrate a softsearch tool in galaxy it takes two input  1)Fasta file  2)Bam file both...
• How To Use Gatk Unified Genotyper With "A List Of Genomic Intervals Over Which To Operate" Option
  Hi, I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option ...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• 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...
• Human Genome Latest Annotaiton
  Hi Jen, I uploaded some fastq files and selected as Genome from the drop down list ""Homo sapiens...
• 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...
• Genomes no longer available after database migration
  I recently moved out production galaxy from one postgres database to another. In the process I ca...
• Reference genome from data visualization
  Hi What I have seen in the tutorials is that you can see the FreeBayes results in IGV but only a...
• RNA STAR -Gapped-read mapper for RNA-seq data (Galaxy Version 2.5.2b-0)
  Hi, Now that Galaxy has introduced RNA Star in their list of tools in NGS: RNA Analysis, I wante...
• Hg19 With Rcrs
  Dear Galaxy,Before the new modifications, i was using hg19 human genome with the rCRS mitochondr...