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• TopHat RNA-Seq FASTQ file not seen
  Hey, I'm trying to use Galaxy to process my RNA-seq data. I have uploaded the fastq file to gal...
• Cufflinks Annotation Problem
  Colleagues, I am having trouble running cufflinks with an annotation file on the public Galaxy. ...
• Fastq And Index File Upload Problems
  I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using a newly assembled ...
• RNA-seq data extract
  Galaxy upload RNA-seq data（.gz） need to extract it？ How to extract RNA-seq data（.gz）？ Thanks!
• Modifying GFF files
  Hi: I am working with a GFF file, which is missing 5' UTR annotations. I thought I might be able...
• Fw: Problem In Data Uploading
  Hi, I am a first time user in galaxy for analysis of my RNA-Seq data. I am facing probl...
• de novo assembly
  Hi folks I would like to use de novo assembly and quantification for mink RNA-Seq data. I am won...
• Merge RNA-Seq files in CLC Genomics Workbench ?
  Hi I now analyzing my RNA-Seq data (illumina, 50bp paired end) using CLC Genomics Workbench to ve...
• Cufflinks assembles very small number of transcripts from RNA-seq data
  I mapped RNA-seq data to reference genome and tried to assemble transcripts using cufflinks.It is...
• Why won't Galaxy recognise uploaded hg19 .fasta.gz file?
  Hi. I'm doing RNA-seq analysis for the first time and want to upload the hg19 genome from 1000 Ge...
• How to obtain more space for raw data and analysis
  Hi I will use galaxy for RNA-seq analysis I start to upload the raw data FatQ file I will reach t...
• Custom genome for galaxy- Ensembl reference genome
  I want to perform a DEXseq analysis on alternative splicing, and it requires to map the RNA-seq d...
• ftp server down?
  Hi: I want to upload my RNA-seq data to galaxy. I can only use the FTP server to upload. But I c...
• bowtie aligner does not see my fastq file?
  Although I could see that the RNA seq data has been uploaded as fast file in the history, I could...
• Galaxy Tool Error Report From Johnwu@Ibms.Sinica.Edu.Tw
  GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the serv...
• low number of assembled transcripts for cufflinks with annotated genome
  So I am pretty new to the bioinformatics movement and am having trouble assembling trancripts usi...
• FIle transfer from GEO to usegalaxy.org
  I'm trying to import some public GEO data into usegalaxy.org - specifically, the mouse RNA-seq da...
• RNA seq analysis for samples from TCGA.
  I got files RNA seq files from TCGA. They are in TAR archive and will extract them. How do I uplo...
• RNA-seq data normalisation with housekeeping genes
  Hi there, I just generated a couple of RNA-seq dataset hoping to identify the differentially exp...
• Loading Fasq.Gz Files Using Ftp
  Hi I am NEW to RNA-seq data and galaxy programs. When I try to up-load the RNA-seq data using Fil...
• Trinity with multiple datasets
  Hello, I am running trinity on 4 data sets (2 left reads, 2 right reads) and I want it to be com...
• Cufflinks Error In Galaxy
  Hi galaxy dev team: I just installed galaxy on my ubuntu box and tried to do RNA-seq analysis ...
• Where can I find the Trinity statistics?
  Hi, This is maybe a stupid question, but I am new to RNA sequencing and the Galaxy environment -...
• HG38 .gtf file
  Hello. For practise, I am running an RNA-seq analysis on some of the RNA-seq data from Illumina ...