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• 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 "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...
• Tools appearing/disappearing from tool panel (FreeBayes and BamLeftAlign)
  Hi All, I am seeing a problem where the tools FreeBayes and BamLeftAlign (under the NGS: Variant...
• passing parameters to workflows via API
  Hello, I've two questions regarding passing input parameters through workflows API. I'm using th...
• 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 "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 "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 "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 "Tophat2" tool
  My Galaxy Tophat2 program is not running. Is there is any server problem   Tool name: Tophat2 ...
• 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 "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...
• problem with "join" tool
  Dear All, I've got problem with "join" tool. When I'm trying to combine two datasets, I obtain ...
• Need help with "Map with Bowtie for Illumina" tool - Methanosarcina acetivorans
  Hi there,  Would it be able to include "Methanosarcina acetivorans C2A" in the Reference Genome ...
• Need help with "Map with Bowtie for Illumina" tool
  How long will "This job is waiting to run" take?   Tool name: Map with Bowtie for Illumina Too...
• 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 "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 "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 "Varscan" tool
  In my browser window, Varscan for variant detection does not allow me to add datasets. What is wr...