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• 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...
• How do I get reference genome?
  There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome....
• NGS:mapping against maize reference
  Hi, when I select NGS:Mapping / Bowtie2 or BWA, in order to align sequences from GBS against a r...
• Need help with "Bowtie2" tool
  Hi, is there a way to upload our own reference genome?   Tool name: Bowtie2 Tool version: 0.2 ...
• Adding Reference Genome
  Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in gala...
• No chicken reference genome (galGal4) for Bowtie2 - map reads against reference genome
  Hi, I cannot find the chicken (galGal4) reference genome when I run Bowtie2 - map reads against ...
• Bowtie2/Samtools files are not visualized with Trackster: Fatal error Exit code 255 ()
  I am trying to map 8 paired-end reads on to the same reference custom-build genome. Each of these...
• Yeast genome reference in Bowtie2
  I am trying to do some data analysis of my Chip Seq data in yeast. And I stuck at the alignment s...
• Upload Jatropha Reference genome for Bowtie2
  Hi Team Galaxy, I would kindly request you to upload Jatropha curcas reference genome in Galaxy ...
• Genome build accession for Galaxy build-in genomes
  How can I find exact genome build (NCBI accession number, like GCA_000001405.17) for build-in gen...
• Question On Galaxy Reference Genome Window
  Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how...
• How to make Bowtie2 align a specific number of nt
  Hi, I am trying to align some tumor miRNA sequencing data to a viral genome using Bowtie2. In o...
• I used tophat and give mistake Error: segment-based junction search failed with err =-5
  In my local galaxy , I used Tool Shed TopHat Gapped-read mapper for RNA-seq data (Galaxy Version ...
• Visualizing BowTie2 BAM File?
  Good Morning: I am new to Galaxy, and have a question about the BowTie 2 BAM file.  I had BowTie2...
• TopHat Error stating that (installed) Bowtie2 is not installed
  I tried to try 'TopHat (v.2.1.0)' locally to align some RNA-Seq data to a reference human genome....
• 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...
• Questions about addition of reference genome in Bowtie2
    Now I'm going to analyze my ChIP-seq data with Galaxy, but there is not the species I want on ...
• Support for loxAfr3 in Tophat2 and Bowtie2
  To Whom It May Concern, I'd like to use Tophat2 and Bowtie2 for RNA-seq analyses with the most r...
• Bowtie2 not working
  Dear sir, i have uploaded some RNA Seq data and done with FastQc. I wanted to map the reads to m...
• Trying to upload own reference genome to use in Bowtie2 and BWA aligner, having trouble with FTP filezilla
  Hello there, i am new to galaxy, and so far im loving all of the features. As a final year stude...