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• How to upload a reference genome
  Hi!, I am a new user in the Galaxy project and I want to map my reads with a genome that is not i...
• 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...
• [Fwd: Re: [Genome] Chimp Assembly 2 Pairwise Alignments]
  Hi there, further to the query below, I'm trying to follow the steps outlined in the email below ...
• Settings in workflow
  Hello, My workflow includes Bowtie and htseq-count and I'd like to be able to set the reference ...
• Addding iGenomes inGalaxy
  If i download iGenome of particular species (In may case Chicken) from http://ccb.jhu.edu/softwar...
• Is it possible to add custom JavaScript tool in Galaxy
  I'm looking into adding a custom tool into Galaxy that makes a HTTP request to an API end point, ...
• Viral Metagenomics
  Hi, Can you please tell me how to work with viral metagenomics in Galaxy? When uploading the d...
• Re: Trouble Getting Tophat To Run On Built-In Index Genome
  Hi Noa, There are two issues: Using the correct genome and setting up paired data properly. 1 -...
• --fr versus --rf option in Hisat2
  Hi! We have a library of paired reads generated by the UTF-8'en-us'SMARTer Stranded Total RNA-Se...
• Featurecounts built-in annotation hg38, hg19, mm10, mm9
  "Parameter genome requires a value, but has no legal values defined" stop me from execution. whic...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• why do Galaxy have a reference genome of sheep?
  Hi: I am analyzing RNA-seq data of sheep using Galaxy. But I can not find a reference genome abou...
• Cufflinks in galaxy
  When I am using cufflinks in galaxy the option use reference annotation, when selecting use refer...
• How to use Mothur Unique.seqs
  I see two window 1. Sequences to filter I use this to select sequence(s) of new assembling 2. ...
• GATK tools and reference genomes
  The GATK tools are present as a beta version, and I tried to use selection or filtration, and the...