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• 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...
• Filter For +/- 2-Fold Difference In Expression Levels
  Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I ...
• RNAseq exon count
  Hej, I have an RNAseq dataset (single end) from a mouse model heterozygous for a trapped-gene. Th...
• Constitutive Exon Workflow?
  Hi folks, I'm trying to find over the entire human genome, for each gene, which exons are the mos...
• 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...
• CuffDiff error on Local Galaxy
  HI, I am running local instance of Galaxy on my linux mint system. When I try to run CuffDiff, ...
• Cuffdiff Results Missing
  Hi, I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group one has two replicates ...
• cuff diff output
  HI, I want to use the gene differential expression output from cuffdiff for performing gene onto...
• Cufflinks duplicate GFF ID error - best course of action?
  Hi, I have a question regarding the best way to handle genome annotations that include duplicate ...
• Access to NGS: Differential expression
  How to gain access to the advanced tools in NGS: Differential expression. This is not listed in m...
• Cuffdiff-output file gene differential expression-Degust
  Dear Galaxy team, Is there a tutorial to show how to load and visualize cuffdiff output files (e...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Cuffdiff Fatal error: Matched on error
  Hello, I am doing my first RNA seq data analysis using galaxy. I have assembled my transcripts u...
• 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...
• Galaxy With Cuffdiff Output
  Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc...