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• Galaxy sourcing reference data from location not in data table
  Hi all, I'm having a issue with the picard tools downloaded from the toolshed. When trying to us...
• Genome build accession for Galaxy build-in genomes
  How can I find exact genome build (NCBI accession number, like GCA_000001405.17) for build-in gen...
• Reference genome for RNA STAR
  Hi, I am trying to use STAR for aligning RNASeq data but it doesn't have any reference genome. I...
• RNA-STAR Failing using hg38 but works for hg19
  Hi, I am trying to align two collections of 4 single-end RNA-Seq fastq files (8 fastq files tota...
• Loading human hg38 onto local instance
  Dear Galaxy Team I have a Galaxy Instance loaded onto my computer and have been trying to create...
• RNAseq: RNA STAR ---Mapping to a viral genome
  Hi, I am analyzing an infection time course in a human cell line transduced with Vaccinia virus. ...
• RNA-star: splice junction
  Hello, I am new to RNA-seq data. I am using the built-in index and using the reference genome wi...
• Reference genome in Galaxy cloud for RNA-seq
  Hi. I am trying to align paired end reads from human samples using Tophat2 in Galaxy cloud. Wou...
• Bias Correction : Locally cached human reference sequence data
  For a cufflinks run, Galaxy detected up human (homo Sapiens) hg19 for the locally cached referenc...
• Star-Fusion last-matching gene pairs file
  Hello, Could you please clarify the correct file to use as a last-matching gene pairs file for S...
• SnpEff supports only genomes of two species?
  Under usegalaxy, I was trying to use SnpEff to annotate my VCF, but the genome dropdown list show...
• Add RefSeq ID to VCF file
  Hello! I am working with whole genome sequence of homo sapiens. I aligned my sample data with hg3...
• Tophat in Cloudman: missing built-in genome
  Hell all, After several days of struggling, I finally managed to set up a Galaxy instance in Clo...
• Getting all unmapped reads
  I have a fastqsanger dataset from an RNAseq experiment, and I am trying to remove contaminating h...
• HISAT error msg or 0% alignment.
  Hi, I'm very new to Galaxy and RNA-seq in general. I can't seem to figure out why we are getting ...
• Can I make a 'gene model for splice junctions' for use in RNA STAR inside Galaxy?
  I am a complete newbie to RNA-seq analysis. I am trying to follow online tutorials etc to learn t...
• Checking coverage of yeast whole genome sequencing data
  I have WGS data (2x150b paired end NextSeq reads) for Yeast (sacCer3) and would like to know how ...
• Problem with Data Manager "Create DBKey and Reference Genome"
  Hi everyone, I had a bug when I tried to use the data manager "Create DBKey and Reference Genome...
• Is the RNA STAR aligned file already been sorted?
  Also, I see unknown contigs that are not present in my chosen reference hg38 gtf file (Gencode.v2...