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• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...
• 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...
• Zebrafish Genome on HISAT2
  Hello, The reference genome for zebrafish (D. Rerio) is missing from Hisat2. Could this be added...
• HISAT2 reference genome unobtainable
  Trying to use HISAT2 - no reference genomes are available, how should I report this? Many thanks,...
• How can one adjust sensitivity and the extent of mismatch between reference genome and target sequences in a data set when using HISAT2 aligner?
  I have two questions concerning the HISAT2 tool installed in Galaxy: 1. How can I increase sens...
• Arabidopsis genome to HiSat2
  Would it be possible to get the Arabidopsis thaliana genome pre-loaded into HISAT2 on Galaxy Main...
• Add reference genome
  Hi, Is it possible to add Arabdiopsis as reference genome to the build in set for the hisat2 pro...
• Adding a reference genome to a local Galaxy
  Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that t...
• 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...
• Is HISAT2 working in GALAXY?
  I always can not choose from the build-in reference genomes. Anyone has the same problem here? o...
• 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...
• HISAT2 incompatible with CuffDiff ?
  Hey I'm trying to compare the transcript expression levels between two conditions. I have put ...
• 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...
• How to prepare FastQ files for HISAT2
  Hi there, Should I be preparing or otherwise cleaning fastq files before I try to align them to ...
• Im trying to use HISAT2 but cannot get the job done!!
  Im trying to use HISAT2 but cannot get the job done!!! this message is given: "This is a new data...
• instructions for fetching and install mm10 genome and hisat indexing for local galaxy
  Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing ...
• Pair end alignment using HISAT2
  Hi, I have a FASTQ file that is a paired library. I want to align this FASTq file to Hg19 genome...
• 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 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• HISAT2 and custom reference genome
  Hi! I want to perform HISAT2 aligment in galaxy using a custom genome. In this case I want to us...