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• Cuffdiff issues: test_stat = -nan
  Hi, When I ran Cuffdiff, I had 92 genes that had the problems with the "test_stat" column. Thes...
• Cuffdiff issues: test_stat = -nan
  Hi, When I ran Cuffdiff, I had 92 genes that had the problems with the "test_stat" column. Thes...
• Exceptionally High Rpkm Values Of Mirna And Other Short Genes In Cuffdiff'S Output
  Hi all, I have been analyzing my RNA-seq data on mouse tissues. My RNA-data is single-ended and 5...
• q values p values from Cuffdiff are same for different samples
  I ran some human samples for mapping with BWA, Cufflinks, and Cuffdiff. When I looked at signific...
• Problem in cuffdiff
  Hi everyone...after doing cuffdiff when viewing the data in tabular format of gene differential e...
• Problem With Cuffdiff
  Hy guys, I am performing some RNA sequencing. I am using a gtf file as a reference annotation for...
• How To Extrapolate Differentially Expressed Genes After Running Cuffdiff?
  Hi guys, have a question about the cuffdiff output "differential expression testing". For most o...
• Mutliple UCSC gene names in RStudio Data Table
  Hi there, I am using the cummeRbund package in R Studio on my personal computer to analyze diffe...
• More Problems with Cuffdiff
  Hope someone can help, I have some RNASeq data and I have 2 groups (Control and Treatment) each ...
• Inconsistent Cuffdiff
  dear all these are the cuffdiff outputs for the same transcript/gene (one isoform only): transcr...
• 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...
• How To Replace Ensembl Gene Id With Gene Names In Cuffdiff Output?
  Hi all, I had the following Cuffdiff output from genes defferetial expression testing: test_id ...
• Cufflinks and gene name
  Hellos everyone, I know there's many posts regarding this question but I still have found myself...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• A Question About Cuffdiff "Values"
  Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of...
• Counts vs FPKM
  I was able to retrieve the counts from my RNAseq analysis via Cuffdiff so as to compare with the ...
• 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 ...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...