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• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• Replicate Common Gene Names
  This is somewhat Galaxy related, but more of a general question. I did all of my mapping and ini...
• Finding Constitutive Exons Using Expression Data
  Hi, I'm trying to find over the entire human genome, for each gene, which exons are the most cons...
• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• RNA-seq analysis for a small number of genes
  Hi all, I am new to RNA seq analysis and want to look at the expression of a small number of gen...
• Cuffdiff-differential gene expression-NOTEST
  Hi I am just starting up and getting to know and analyze my data from the RNA-seq. I have 2 biol...
• RNA-Seq analysis for 2 genes
  Hi, I did RNA-seq for 20 samples and I am interested in the differential expression of normal tra...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• cuffdiff output to gene enrichment analysis
  Hi all, I successfully ran my RNA-seq data through the entire tuxedo suite on galaxy. I would li...
• Cuffdiff: selecting replicates in a different order gives me different numbers of differentially expressed genes. Why?
  I have two groups with four biological replicates per group. I tried comparing group 1 to group 2...
• Rna Seq Analysis
  I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the ...
• htseq read counts zero
  Hi, I have imported some fastq files (homo sapiens) from http://www.ebi.ac.uk/ena/data/ to Galax...
• Htseq-count: How to add id attribute and additional attributes in Galaxy (RNA-seq)
  Hello, I am working with a bacterial genome. I'm using DESeq2 for differential gene expression an...
• Comparative Analysis
  I need to compare genome sequences of several Salmonella enterica serovars. I will be looking fo...
• Critical Feedback
  This student was more adventurous. I think he actually could do more of what he tried with more e...
• Inbuilt reference genome
  Hi, I ran a top hat analysis on samples, but after the cuffdiff step, I do not have any genes an...
• Cufflink Workflow
  Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GT...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...
• Micro-RNA Host Genes
  Hi, I have carried out differential expression analysis using Deseq2. One of the most differentia...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• Differential expression from FPKM
  Greetings, I've been using some of galaxy tools for the last months, namely for tuxedo pipeline. ...
• RNA-seq Analysis after CuffDiff: Clustering, etc
  Hello -  I am very new to RNA-seq analysis and am trying to figure out my next steps. I ran Toph...
• How to map RNA-seq reads to an annotated reference genome in GFF format
  Hi, I am trying to map RNA-seq reads to a GFF annotation file I created using tophat2 through Ga...