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• Questions On Cuffdiff Output And Browser Visualization
  I would really appreciate someone's input on some issues I am having with my cuffdiff output for ...
• differential expression exon-level
  Hi everybody, I've been using cufflinks in order to perform differential expression between to g...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Gene Or Transcript Differential Expression Testing
  Hi, I am a bit confused about two outputs of cuffdiff: If I want to see if two samples, e.g. trea...
• cuff diff output
  HI, I want to use the gene differential expression output from cuffdiff for performing gene onto...
• Tarcking ID in cuffnorm output and TestID (geneID) in cuffdiff output, are they the same?
  Dear all, I found in the output of cuffnorm there was no locus information corresponding to my d...
• The giant different FPKM value of same gene between cufflink and cuffdiff.
  It differs a lot (10 times as large) between cufflink outputs "gene_FPKM tracking" and cuffdiff o...
• Different RNA-seq result when I look at the gene_differential file and the transcript_differential file generated by cuff-diff
  Hi, I am wondering what is the exact difference between the gene list of the **transcript differ...
• Cuffdiff Results Missing
  Hi, I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group one has two replicates ...
• Cuffdiff Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• Comparing FPKM Values Between 2 Cufflinks Outputs
  Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 sa...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• Inconsistent Cuffdiff
  dear all these are the cuffdiff outputs for the same transcript/gene (one isoform only): transcr...
• Regarding A Cuffdiff Output
  Dear galaxy users Hello. I have a quick question about Cuffdiff analysis. I have obtained two SR...
• Analyzing CuffDiff output
  Hi All,   I'm a grad student at the University of Alabama at Birmingham using galaxy for the fi...
• cufdiff output-cutoff pvalue and parameters for differential expression
  dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run...
• Problem With Repeated Genes In Cuffdiff'S Output
  Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression a...
• Gene And Transcript Names From Cuffdiff
  Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one ...