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• Bowtie for Illumina using reference genome of pisifera oil palm tree
  How I can map reads against pisifera oil palm tree genome or against scaffolds? Thank you for a ...
• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...
• How do I get reference genome?
  There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome....
• 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 ...
• GATK tools and reference genomes
  The GATK tools are present as a beta version, and I tried to use selection or filtration, and the...
• Listing genome reference
  Hi, I would like to map reads against genome reference but my genome of interest is not listed. I...
• Problem with custom reference genome
  Dear all, on our local galaxy-docker-stable instance I would like to include additional referenc...
• Aligning Against Multiple Reference Sequences
  Are there any tools in Galaxy to align short reads against multiple reference sequences? I have ...
• 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...
• GATK Select Variants Reference Genome
  Hi, I'm trying to use GATK Tools Select Variants on VCF files of whole genome sequencing data, ...
• galGal5 reference genome and indexes
  Hi I'm interested in the new Galgal 5 assembly obtained in dec2015, for the moment it is only pos...
• Need help with Circos plotting of snps on Galaxy
  Please help me to make a Circos plot of snps against the reference genome on Galaxy. I have a bed...
• 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 ...
• Reference genome from data visualization
  Hi What I have seen in the tutorials is that you can see the FreeBayes results in IGV but only a...
• Creating consensus sequence after mapping
  Greetings, I would like to know how to create contigs, or DNA consensus sequence after mapping t...
• Cannot select the S. cerevisiae reference genome (sacCer3) for "Map with Bowtie for Illumina" in a saved workflow
  I have a saved workflow involving a Map with Bowtie for Illumina step in which I want to map read...
• Reference genome absent
  Dear Biostar, For mapping our paired end reads against horse, we are unable to find a reference ...
• Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'
  Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to 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...
• Downloading Reference Sequences And Other Questions
  Hi I have a few questions 1. I am trying to use Bowtie to map my data using a reference genome. ...