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• Issue visualizing RNA-seq HISAT outputs in UCSC Genome Browser
  Hello, I've used Galaxy to run HISAT alignments and Picard marked duplicates on my RNA-seq file...
• hisat2 index issue (I think)
  Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga...
• 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 ...
• HISAT2 input to StringTie with UCSC mm10 or ncbi refseq GTF produces error message
  Hi, there, rerun HISAT2, tried to run Stringtie for TPM, when running only HISAT results as i...
• Error with BWA in local Galaxy
  Hello, I´m new using Galaxy and would really appreciate some help. I´m trying to run BWA in my lo...
• TopHat2 run with the error message "The Cluster DRM System has terminated this Job"
  Hello, I use Galaxy regularly, and used TopHat2 earlier without any problem. However, just a day ...
• mothur silva.nr_v132.align datasets etc
  Good morning, I am trying to run the mothur command align.seqs using the NGS: Mothur tool. I kee...
• HISAT problem on local galaxy
  Dataset 33: HISAT on data 3Tool execution generated the following error message: Fatal error: Ex...
• Is && needed in xml for seperating lines?
  Hi. I see an example here https://docs.galaxyproject.org/en/latest/dev/schema.html that **&&a...
• Problem with R package for integration
  Hi, I integrated a R tool in Galaxy who works fine, but I added a new functionality needing the ...
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• Empty table output
  Hi all, I'm attempting to run an Rscript that outputs a few tables, but can't get that to work. ...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...
• GRCH37 vs hg19 vs B37 vs canonincal
  In galaxy which human genome should be compatible with GRCH37 annotation for alignment. I uploade...
• FastQ Groomer Problem - Syntax
  Hi, I have searched all over and I cannot find a solution to this. When I run the FastQ groomer ...
• Galaxy Environment variables - can I access DEBUG value from my tool?
  Hi, I couldn't find information about the environment variables that are set when Galaxy runs. I...
• HISAT Error on local Galaxy
  Hi, I am trying to do RNA analysis on local instance of Galaxy running in Linux mint. I have tr...