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• 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 ...
• 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 ...
• Cuffdiff gene ID
  I am using galaxy for differential gene expression analysis. I first converted the ensembl GTF fi...
• 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...
• 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...
• differential expression exon-level
  Hi everybody, I've been using cufflinks in order to perform differential expression between to g...
• Galaxy Tuxedo Protocol Questions
  Hi everybody, I'm totally new to RNA-seq analyses and it's my first time doing this and using Ga...
• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• assembled transcripts TO BLAST2GO
  Hi , i want to compare the ontologies of genes generated from cuffdiff output and use it for BLA...
• Rna-Seq Cds, Splicing And Tss Fails
  Hi all, So I am using cuffdiff to find significant differences between two samples (no replicat...
• Cuffdiff Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• Gene Ontology Help
  To Whom it May Concern: My name is Nicole McDaniels. I am a Ph.D. candidate at Syracuse Universi...
• Is Tss_Id Unique For Each Transcript?
  Dear All, I am reading and comparing the outputs of Cuffdiff. I found there is a "tss_id" column...
• Gene annotation for cuffdiff/cufflink
  I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, an...
• 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...
• Inconsistent Cuffdiff
  dear all these are the cuffdiff outputs for the same transcript/gene (one isoform only): transcr...
• cuff diff output
  HI, I want to use the gene differential expression output from cuffdiff for performing gene onto...
• 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...
• Cufflinks Assigning separate Cuff I.D. to gene that falls within location of known gene
  Hi, I am following the workflow for differential expression analysis using cuffdiff on galaxy as...
• Clustering With Cuffcompare Or Cuffdiff Results
  Dear Sir or Madam, I am planning to do clustering of several libraries based on the output of cu...