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• Help!!! Cuffdiff Log2 Value
  Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expres...
• Cufflinks/merge/diff tools deprecated
  I've been using a HISAT2 -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund pipeline...
• CUFFDIFF SCRIPT path
  I am trying to do RNA seq data analysis I encounter a error in the cuffdiff step stating No versi...
• How do I associate a genome with a BAM file?
  I aligned some RNA-Seq reads to a genome sequence using tophat2 and now cuffdiff complains that t...
• 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...
• RNA-seq data normalisation with housekeeping genes
  Hi there, I just generated a couple of RNA-seq dataset hoping to identify the differentially exp...
• Cuffdiff Gene Fpkm Tracking File- Sorry! I Sent Only A Part Of My Email
  Hello everybody, I'm quite new in NGS world, I'm trying to analize dome RNA-seq data. I followed ...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• 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...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Re: Using Galaxy For Bacterial Rna-Seq
  Bomba, I'm not familiar enough with bacterial/prokaryotic transcriptomes to suggest a possible w...
• Cuffdiff gene name
  Hi! I am analyzing RNA-seq using tophat-cufflinks-cuffdiff, but at the end, in the cuffdiff tabl...
• How to use cuffmerge and cuffdiff
  I am trying use Galaxy to analysis the yeast RNA-seq data. When I want to try the cuffmerge and c...
• Re: Rna Seq Analysis And Gtf Files
  Slim, Please send questions to the galaxy-user mailing list (cc'd) rather than individual Ga...
• CufDiff at usegalaxy.org
  Hello! I'm wondering where CuffDiff has gone under NGS:RNA-seq at usegalaxy.org, has it been dis...
• RNA-seq pipeline standard?
  I'm not following the new trends specifically for rna-seq so are there something more innovative ...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• 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...
• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• Cuffdiff Errors
  Hello, I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 sampl...
• Cuffdiff Output
  Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. ...
• Getting Genome Coordinates for a List of ENSEMBL IDs
  I need to convert a list of ENSEMBL IDs from an RNA-seq dataset to UCSC mm9 genome coordinates. A...