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• 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...
• 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...
• Reference Annotation error using HISAT2
  I keep getting a reference annotation error when I run cuffdiff using HISAT2 alignment files. The...
• Failure to find .bai file index
  I am having an issue with NCBI genome workbench recognizing the .bai index file from a bowtie ana...
• 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...
• 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...
• 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...
• HISAT2/TOPHAT alignment to a Rabbit Genome
  Hello, I have multiple samples of human stem-like cells that were retrieved from an animal model....
• RNA-seq analysis- HiSat2 and Cufflinks
  Hello, I am new with RNA-seq data analysis. I am using Cygwin software in order to create a Linu...
• HISAT2 gzip: input_r.fastq.gz: not in gzip format
  Hello, I have been trying to use HISAT2 to to align RNA-seq ENCODE data which I download on my de...
• Other uses than genomic data
  Hi, I am new to using Galaxy, I am wondering if the functionality that is being used for the dat...
• HISAT2 reference genome unobtainable
  Trying to use HISAT2 - no reference genomes are available, how should I report this? Many thanks,...
• Arabidopsis genome to HiSat2
  Would it be possible to get the Arabidopsis thaliana genome pre-loaded into HISAT2 on Galaxy Main...
• Tophat not recognizing the ref genome I loaded
  I am trying to run Tophat as I did in a previous analysis using the same ref genome. It is a fas...
• Problem with loading histories
  I am taking the Coursera course "Genomic Data Science with Galaxy."  I noticed from the beginning...
• 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...
• 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 and Rat annotation database
  For HISAT2 I am using the Rat fasta annotation file. Is it supposed to be any particular one? A...
• Poor overall alignment rates
  I am having problems with the alignment process for some data that I obtained through NCBI GEO da...
• SNP tool (Amino acid change) throwing error
  Hi I have discovered some 240,000 SNPs and am using the **"amino-acid changes caused by a set of...
• Fatal Errors occurring with htseq analysis
  Hi, I am in the process of analyzing some RNAseq data. I uploaded the data and successfully mapp...
• SAM-to-BAM (NGS: SAMtools)
  I am trying to convert my SAM file to BAM file and I want to use the built in genome, but there i...
• Error with htseq-count
  When I run htseq-count in galaxy I keep getting errors. The line in the history will look as foll...
• Mapping (with HISAT2 / Bowtie) on custom genomes yields always 0 matches
  Hi, I've the following problem. I'm using HISAT2 and Bowtie. I'm using a gene with 1200 nucleoti...