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• 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 "patmatdb" tool
  Everytime I try to use open brackets or "{ or }" I get an error message.  Would really like to be...
• 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 "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 "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 "Filter SAM" tool
      Tool name: Filter SAM Tool version: 1.0.0 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/sa...
• Need help with "FASTQ Groomer" tool
      Tool name: FASTQ Groomer Tool version: 1.0.4 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam...
• 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 "Variant Annotator" tool
    What is the meaning of this error" History does not include a dataset of the required format /...
• Need help with "Tophat2" tool
  My Galaxy Tophat2 program is not running. Is there is any server problem   Tool name: Tophat2 ...
• Need help with "Cufflinks" tool
  What value does Galaxy use for -max-bundle-frags? I could not find a way of changing this paramet...
• 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 "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
  biuld index   Tool name: Map with BWA for Illumina Tool version: 1.2.3 Tool ID: toolshed.g2.bx...
• Need help with "patmatdb" tool
  where to find the motif detail for plant membrane proteins   Tool name: patmatdb Tool version:...
• 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 "Map with BWA for Illumina" tool
  index   Tool name: Map with BWA for Illumina Tool version: 1.2.3 Tool ID: toolshed.g2.bx.psu.e...
• 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 "MACS" tool
  Hi everyone, I don't quite understand the meaning of the parameters of this program.  1. What i...
• Need help with "MPileup" tool
  I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium...
• Need help with "Tophat2" tool
  I was trying to repeat one tutorial on RNAseq (RNASeqDGE_ADVNCD_Prep). In the TopHat2 section, I'...
• 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 "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 "Cuffcompare" tool
  Dear Jennifer,           We did not get the right information what we are looking for. The only ...