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• Bowtie2
  Hi All I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq file...
• I do not see and cannot access 'Cloud' drop down menu from use galaxy home page
  I do not have Cloud as one of my drop down menus at the top of web page use galaxy.org. What can ...
• Display a file stored in database
  hii I am integrate a softsearch tool in galaxy it takes two input  1)Fasta file  2)Bam file both...
• disk quota is low
  Hello, While RNA-seq data have been running, the sign came 'You are over your disk quota. Tool e...
• Galaxy Not Showing My Reference Genome In Drop Down For Bowtie
  Hi guys, As shown in the attached screenshot I uploaded a fasta file. And I want to use it as m...
• Remove genomes from tool drop down menus
  I really hope someone can help. I have a local instance of Galaxy. I have genomes that appear in ...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• Dataset Does Not Appear In A Drop-Down Menu Of A Tool
  Hi, I just started using the main galaxy instance. I uploaded via FTP and imported several FASTQ...
• BWA-MEM Tool not recognizing fastq inputs
  I am attempting to use the NGS mapping tool BWA-mem. I have uploaded my reference genome, in addi...
• Fastq Joiner
  I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joine...
• Using reference file in Indel realigner under locally cached option
  Hi , I am trying to use indel realigner before somatic variant calling for tumor-normal pair. I ...
• Adding reference genomes to local instance of Galaxy using Rsync
  Hi everyone, We were finally successful in downloading selected reference genomes as they appear...
• How To Use Gatk Unified Genotyper With "A List Of Genomic Intervals Over Which To Operate" Option
  Hi, I would like to run "Unified Genotyper" on a region of a BAM file, I see the advance option ...
• GEMNI doesn't recognize hg19 VCF file!
  I am trying to import my hg19 variant call file, but on GEMNI tab, it appears it doesn't recogniz...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• no fastqsanger dataset available after successfully uploading fastqfile
  I uploaded the fastq file to galaxy successfully and can view its detail. When I use 'compute qua...
• Fastq Joiner Problem
  Hi, I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq j...
• FASTQ Joiner or Interlacer problem
  Hello everyone, I am trying to use the FASTQ interlacer or joiner on my pair end read files. Aft...
• How to specify output format by a drop-down box?
  Hi. How to let the user select from a drop-down box for the desired output format (formatA or for...
• 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...
• Changes in admin menu - Upload files
  Hi, I manage a galaxy instance on a local server and I want that users use only the "filesystem ...
• Incorrect Permissions When Uploading Files
  Hello, I think there is a problem with the way permissions are set when uploading files. As admi...
• 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...