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• Need help with "Merge BAM Files" tool-large number of files to merge into one
  HI  I want to merge at lot >40  of individual bam files into one.   Is there an easier way t...
• Need help with "Variant Annotator" tool
    What is the meaning of this error" History does not include a dataset of the required format /...
• 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 "Tophat for Illumina" tool
  Dear All, Hello amazing Galaxy team members  now i have 14 manipulated fastq files 7 forward an...
• 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 "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 "Reverse-Complement" tool
  I have a fastq file uploaded and would like to get the reverse-complement. But it was not recogni...
• Need help with "Reorder SAM/BAM" tool
  HI am trying to reorder a SAM file output from BWA. So I can use it in GATK.   However I get the...
• Need help with "Cufflinks" tool
      Tool name: Cufflinks Tool version: 0.0.7 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuf...
• Need help with "SICER" tool
  How can you add a genome to SICER in Galaxy?     Tool name: SICER Tool version: 0.0.1 Tool ID...
• 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 "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 "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 "Map with Bowtie for Illumina" tool
  nothing happened when clicking the input file dropbox, can not upload files.   Tool name: Map ...
• Need help with "Cufflinks" tool
  Hi, How long does it take usually that GALAXY upgrade with a new version of Cufflink (version 2....
• How to configure genome in "Map with BWA" (existing tool) after adding it to my local section
  Hi. I have added the lines below to the section I made in config/tool_conf.xml file and "Map with...
• Need help with "FastQC:Read QC" tool
  I have collected the raw data for my RNA-seq project. This dataset includes short DNA sequences o...
• 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 "Fetch taxonomic representation" tool
  Hello, i need to fetch the HCV sequence from my data set how can i use the fetch-taxonomic-repre...
• 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 "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 "Filter sequences by length" tool
  How do I upload my fasta file? No options appear when I click the down arrow? Thanks! Jackie ...