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• unable to input file in trimmomatic
  Preparing for trinity analysis I try to trim questionable 5' bases. Trying to use 'Trimmomatic', ...
• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...
• how can I use a custom adapter sequence in trimmomatic while in Galaxy?
  Hi, I want to use a custom adapter sequences in trimmomatic. But when I upload a fasta file, the...
• Cannot select data sets in local galaxy sever
  Hey, So I've installed a local galaxy server in order to helpout processing some large data we h...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• Can't change datatype
  Galaxy won't let me edit attributes even though fastq file is not in use. I'm trying to change to...
• Can't configure admin menu - Local galaxy [SOLVED]
  Hello :) I'm trying to configure galaxy admin menu, locally, so I can install new tools. I've lo...
• Upload large files to localhost
  Hi, I'm trying to upload some large reference files to my galaxy localhost, but i can't figure ou...
• Running Trimmomatic on loop for Paired End
  I'm need to do trimming for Paired End. Is there any way around where I can run the trimmomatic ...
• Visualizing RNA STAR Bam file
  hi I'm working through the RNA-seq tutorial using the Pasilla knock down example. I have made i...
• Can't find a universe_wsgi.ini file
  I installed Galaxy using Mercurial (and re-installed several times to try and resolve this issue)...
• input file types to DESeq on the cloud
  Hi there, I've had a go at using the Ratsch lab DESeq tool but it seems to require your input fi...
• Data Files For Fundo Tool In Human Genome Variation?
  Hi, I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block...
• Fastq File Generated By Samtools Can'T Be Recognized
  Good day. I'm trying to use Galaxy's FASTQ to FASTA converter. However, the fastq file I generat...
• Change Format With "Edit Attributes"
  Hello, I'm trying to change the format to the output files from Barcode splitter from FASTA to F...
• How do i remove multiple adapter sequences from my RNAseq reads?
  Hi there, I want to remove the universal adapters as well as the index adapters in each data fil...
• Read_Group_Tracking Files Are Not Enough For Cummerbund Visualisations On Replicates?
  Hi, Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if these files ar...
• NGS: QC and manipulation
  Hello, I'm a beginner (my email zare@ibt.lt) of using Galaxy. I tried to use Trimmomatic or Trim ...
• Megablast is not working
  Hello, I've seen in previous posts that there was some problem with the megablast tool some mont...
• Can't filter unmapped reads in my BAM file
  Hello everyone. I'm a newbie in bioinformatics and I'm trying to filter a BAM file using the Gala...
• Used space in account never goes to 0%
  I've had a problem with my Galaxy account for a few weeks now, where the amount of space used sta...
• Importing a Repository Capsule
  Hi all! I'm trying to get the biopython package onto a private toolshed, but having trouble with ...
• 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 ...