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• Need help with "Cufflinks" tool
      Tool name: Cufflinks Tool version: 0.0.7 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuf...
• "Realigner Target Creator" tool on usegalaxy.org Locally cached reference unavailable
  HI  I have a bam file generated using a cached reference  (not a user custom one).  However if I...
• error using variant recalibrator in galaxy
      Tool name: Variant Recalibrator Tool version: 0.0.4 Tool ID: toolshed.g2.bx.psu.edu/repos/...
• Need help with "FASTQ to FASTA" tool
  Excuse me, How can I submit my local FASTQ files to convert with this tool?   Tool name: FAST...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi!  I entered a vcf file into the annovar tool.  It looks like it ran and tells me then number o...
• 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 "Merge BAM Files" tool
  Can I merge more than two BAM files together at once? I have three Bam files that I need to merge...
• 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 "Trim sequences" tool
  is it normal it does not work on fastq files? I had to convert my fastq into fasta in order to t...
• Need help with "Tabular-to-FASTA" tool
  I am trying to use this tool to convert genes that are in excel to fasta format.  I saved as tab ...
• 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 "Unified Genotyper" tool
  Every time I try to use the Unified Genotyper Tool under GATK, I receive the following error mess...
• Need help with "Varscan" tool
  In my browser window, Varscan for variant detection does not allow me to add datasets. What is wr...
• Need help with "FASTQ Trimmer" tool
  FASTQ Trimmer seems unable to recognize my FASTQ files as input. For e.g. I carried out FASTQ to ...
• 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...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi there, When I open Annovar annotate VCF tool on Galaxy I cannot visualize any option for the ...
• Need help with "Create a BedGraph of genome coverage" tool
  Hi there I am trying to calculate the coverage of my alignment based on the BAM file using "Crea...
• 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 have uploaded .fastq files successfully but the "FASTQ file" drop-down list doesn't show my .fa...
• 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 "Bowtie2" tool
  .fq file is saved in the history, but does not appear on the 'FASTQ File' dropdown list?   Too...
• Need help with "Feature coverage" tool
  for what purpose it is and what type of input data it needs   Tool name: Feature coverage Tool...