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• Drosophila Yakuba Reference Genome
  Hi, Could galaxy include the Drosophila yakuba reference genome for use with Tophat? It's not lis...
• update drosophila genome to dm6
  The Drosophila genome has been updated to dm6. However, the Galaxy still only use dm3. Many gene ...
• Fetch alignments using stitch Gene Blocks but all the gene-sequences are in '--------'
  I was using the GALAXY project (https://usegalaxy.org/) online server, the section is Fetch align...
• Can't choose custom genome for bed files used in Stitch Gene Blocks
  I'm trying to extract and stitch maf blocks from the UCSC Drosophila alignment that uses the most...
• expression of transgenes
  I work with Drosophila transcriptome and sometimes I need to evaluate expression of artificial tr...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Getting Sequences For Multiple Species From Ucsc
  Hi all, I am wondering if there is a way to download sequence information from UCSC into Galaxy ...
• D Mel Reference Genome For Mapping
  Dear Galaxy devs, Would it be possible to include drosophila Melanogaster (dm3) genome for mappin...
• Bed12 Format For Stitching Blocks Given A Set Of Coding Exon Intervals
  Hi Galaxy, I am trying to stitch together MAF alignments for the coding sequence for a few genes...
• Problems displaying data when using Drosophila dm6 reference genome
  I have been trying to analyze data using the most recent Drosophila genome version (dm6). Despite...
• Cufflinks error when trying to align against genome
  I am working with tophat2 and cufflinks in order to try to align RNA-seq reads against an assembl...
• Fetching Promoters
  Hello, Is there a way to fetch the promoter regions for homologous genes from different species....
• Bedtools / FisherBed reference genome
  Hi, I was trying to run the FisherBed tool from the BedTools on the main galaxy server (usergalax...
• Analyzing ChIP-seq data from HiSeq 3000
  I have acquired ChIP-seq data from an Illumina HiSeq 3000. I have followed the analysis workflow ...
• Help with downloading files from EBI SRA
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• CuffDiff error, "Uncaught exception in exposed API method," job runs, but no results
  Hello, I’ve run into a problem while analyzing some RNAseq data on usegalaxy.com. I am looking...
• GTF/GFF file generation
  Hi galaxy team, I want ask how can I generate the gene annotation GTF/ GFF files? My studied o...
• RNA seq analysis
  i have done RNA seq on S2 Drosophila cells and want to check differential expression. I have my d...
• 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...
• Generating Pileup For Snp Analysis
  I am a new user to Galaxy, and I was hoping someone might be able to help with this small problem...
• cufflinks splicing analysis drosophila - 'notest' in output
  Hi everyone, I'm attempting to use cufflinks to examine alternative splicing in my RNAseq data f...
• 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...
• How to install a genome (ce10) to local Galaxy
  Hello, I want to install a genome (ce10) to local galaxy instance. I am the admin of the local g...