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• How do I get reference genome?
  There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome....
• Galaxy tool multi-threading
  I have a local instance of galaxy running on a PC with 4 cores (8 threads). When I run a blast, ...
• Tophat can't see the build-in reference genome?
  I successfully fetch an hg19 and build an bowtie2 index with Data managers. Bowtie2 can see the r...
• Tools not installing in local galazy
  I'm trying to get galaxy running locally but when I try to install new tools the dependencies don...
• bowtie2 output only mapped reads --no-unal option
  Hi, I've been trying to run the galaxy bowtie2 tool and couldn't find an option to report only a...
• Bowtie2 not working
  Dear sir, i have uploaded some RNA Seq data and done with FastQc. I wanted to map the reads to m...
• How to check unaligned reads?
  I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against ...
• using SamToFastq 1.136.0 in Galaxy workflows
  Hello, How can I connect in the workflow SamToFastq and Bowtie2 tools in Galaxy? I am trying to ...
• Trying to run a Tophat on a local galaxy server but it gives me an empty bam file and following message: galaxy_27.sh: line 29: bowtie2-build: command not found
  I am trying to run a Tophat on a local galaxy server but it shows a following message. I guess I...
• Quality metrics of ChIP-seq BAM files??
  Hi all, I'm a real beginner in the field of ChIP-seq analysis and bioinformatics in general (so ...
• Multiple fastq file for mapping with Bowtie2
  Hi,   I have some amplicon sequences for 144 samples that I would like to map on to a reference...
• Fetch taxonomic representation tool error - missing lines
  Hello, I have been using the Fetch taxonomic representation tool from Galaxy online to retrieve ...
• Loading human genome hg38 reference sequence- completely stuck
  I am running a local version of galaxy (17.09) trying to analyze RNA seq data with Bowtie2, DEse...
• Tools does not recognize input dataset: set proper datatype metadata
  My NGS files are fastq files but not recognized by Bowttie2 or Map with Bowtie for Illumina from ...
• Bowtie2 error on producing results
  Hi All, I'm trying to map a test Illumina sequences on cat genome.. I uploaded may Fasta sequence...
• 3-D PCA plot
  Hi, does anyone know if Galaxy.org can do principle component analysis? my boss asked for a 3-D ...
• local galaxy tophat2 built-in genome
  Hi, I am new user to do bioinformatic analysis and know a little about python. Right now, I succ...
• Reference Genomes do not exist in local Galaxy's Bowtie2
  Want to use reference Genome hg19 for Bowtie2 from a local instance of Galaxy. The pulldown for s...
• Simple question please...how to generate BED and GFF files...
  **Simple question please...how to generate BED and GFF files... I have results from RNA-SEQ (gro...
• Galaxy showing and hiding tools as refreshed?
      I have installed some tools, but when I click on Galaxy logo and on Analyse data I see tool...
• When you go into galaxy main page, under tools/getdata, epigraph server is missing.
  Hello,        When you go into galaxy main page, under tools/getdata, epigraph server is missing...