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• Uploading other Reference genome
  Can I upload my own reference genome, i.e. Toxoplasma gondii to map RNAseq data to?
• Tuxedo_Custome build genome
  I have uploaded tomato genome in GFF3 and FASTA format in galaxy. However, when I run Tuxedo, my ...
• Can a genome that's been released be added so I can map against it
  Hi there, I will be mapping my RNAseq reads to a genome of interests soon. Mapping with Bowtie2 ...
• Problem regarding reference genome
  Hi, I am doing RNA seq. analysis in galaxy (using tophat tool). But problem is that my genome of...
• Adding reference genome to Galaxy
  Hi, I want to add reference genome(hg19) from UCSC main table to my Galaxy account,how can I do t...
• How to add a bacterial genome to Galaxy database?
  I have my ChIP-Seq data on Galaxy but can't map it because the bacterial genome that I am working...
• Addition of Rickettsia prowazekii to Bowtie2 reference genome list
  Can the Galaxy team incorporate Rickettsia prowazekii Madrid E (NC_000963.1) into the reference g...
• Genome mapping with Bowtie 2
  Hello,   I would like to map my data against Mycobacterium leprae TN genome but it is not in th...
• Inbuilt reference genome
  Hi, I ran a top hat analysis on samples, but after the cuffdiff step, I do not have any genes an...
• Run Megablast on Galaxy against local genome
  Hey, Does anyone know how I can run Megablast on Galaxy with a reference genome that is not yet ...
• How to add and use a custom reference genome
  How to import my genome (maize B73v3) into galaxy? I have B73v3 in custom-run UCSC genome browse...
• Builtin genome in Galaxy is not displayed in IGB
  Hi, I mapped my peak using MACS in Galaxy using the built-in genome. I can visualize my peaks in...
• Aachanges
  Hi everybody, Maybe a dumb question but does someone know if we can use the aaChanges tool on a ...
• gtf file error
  Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fast...
• Addding iGenomes inGalaxy
  If i download iGenome of particular species (In may case Chicken) from http://ccb.jhu.edu/softwar...
• Nile tilapia reference genome
  Hi, I'm new in Galaxy, but would like to use the project to analyse some of my data on Nile tilap...
• wig to bigwig format in galaxy, unavailable genome
  Hi, I would like to convert a .wig file to a .bigwig file. Should be straightforward, but I am...
• Best Tophat parameters for splicing
  Hey I was wondering if there are any key parameters to consider for Tophat to maximise my chanc...
• Tool to catalog SNPs
  Is there a way in which I can catalog SNPs on Galaxy? I am attempting to use my BAM file, along w...
• Missing tools for genome assembly
  There is no icon for NGS Analysis in my Galaxy tool list. I can not find Velvet or Spades for gen...
• How to use ANNOVAR with bacterial genome?
  I am trying to automatically generate annotations for a VCF file generated from the Mtb H37Rv gen...
• Custom reference genome for RNA-seq
  I am beginning to analyze some RNA-Seq data and having some difficulties with the custom referenc...