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• Need help with "Bowtie2" tool
  Hi, is there a way to upload our own reference genome?   Tool name: Bowtie2 Tool version: 0.2 ...
• Need help with "Bowtie2" tool
  Although my fasq data is in loaded, why could I not see the fast file in the bowtie2 checkbox? T...
• Need help with "Filter by quality" tool
  Why doesn't this tool recognize my fastq files? It won't let me run the tool on the fastq files I...
• Need help with "FASTQ Quality Trimmer" tool
  I am not able to add my file to this tool.     Tool name: FASTQ Quality Trimmer Tool version:...
• Need help with "Map with BWA for Illumina" tool
  Why can't I import my fastq file from my history? I am in the history with all files - gDNA reads...
• Need help with "Unified Genotyper" tool
  Hi there, I would like to add the file 'dbsnp_137.hg19.vcf' to my GATK unified-genotyper analysi...
• Need help with "Generate pileup" tool
  Dear, What kind of files should i use to "using reference genome" and where get it? I trying to...
• Need help with "Map with Bowtie for Illumina" tool
  nothing happened when clicking the input file dropbox, can not upload files.   Tool name: Map ...
• Need help with "Barcode Splitter" tool
  i uploaded a fastq file of the output from the sequencing but it is not recognized as a "library"...
• Need help with "Feature coverage" tool
  for what purpose it is and what type of input data it needs   Tool name: Feature coverage Tool...
• Need help with "Filter by quality" tool
  which formet this tool gets?   Tool name: Filter by quality Tool version: 1.0.0 Tool ID: tools...
• Need help with "Mark Duplicate reads" tool
  What is the aim of this tool?   Tool name: Mark Duplicate reads Tool version: 1.56.0 Tool ID: ...
• Need help with "FASTQ Quality Trimmer" tool
  I have uploaded my fastQ file but it is not showing in drop down list of fastQ-Quality Trimmer to...
• Need help with "Map with BWA for Illumina" tool
  biuld index   Tool name: Map with BWA for Illumina Tool version: 1.2.3 Tool ID: toolshed.g2.bx...
• Data manager failure to create index(s) in 17.05 local
  Been having a devil of a time getting Galaxy going on a brand new 17_05 installation. I have use...
• Need help with "FASTQ Summary Statistics" tool
  I imported some NGS files from EBI, but they came in the FASTQ.gz format. Is there a way to extra...
• Need help with "Filter sequences by length" tool
  How do I upload my fasta file? No options appear when I click the down arrow? Thanks! Jackie ...
• Need help with "FASTQ Quality Trimmer" tool
  I have uploaded .fastq files successfully but the "FASTQ file" drop-down list doesn't show my .fa...
• Need help with "Unified Genotyper" tool
  Every time I try to use the Unified Genotyper Tool under GATK, I receive the following error mess...
• Need help with "Cufflinks" tool
      Tool name: Cufflinks Tool version: 0.0.7 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuf...
• Barcode limit in "Barcode Splitter" tool
  Hello,  I was wondering what is the barcode limit to be run in the "Barcode splitter" tool. I h...
• Loading human genome hg38 reference sequence- completely stuck
  I am running a local version of galaxy (17.09) trying to analyze RNA seq data with Bowtie2, DEse...
• bwa mem index builder error
  I would like to use the BWA mapper tool so I installed the tool "bwa" from "devteam" from main to...