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• Inconsistent Cuffdiff Output-Corrected Question
  Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following FPKM: ...
• Inconsistent Cuffdiff Output
  Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following: trea...
• Cuffdif Output Notest
  Dear all, I have Illumina RNAseq data and want to look for differences in gene expression betwee...
• DIfferent outputs from Cuffdiff using different genome files
  I am analyzing gene expression changes after siRNA knockdown (2 relicates each, control and gene ...
• Cuffdiff-Cummerbund With Biological Replicates Problem
  I'm trying to run Cuffdiff on a set of 10 human samples with biological replication then download...
• co-variance in DESeq2
  Hello all, I have got some RNAseq results back from a group of patients and a group of controls...
• 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...
• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• Cuffdiff Output
  Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. ...
• Cuffdiff-output-couldnot find fasta record for a scaffold
  Dear Galaxy team When i ran cuffdiff for my merged transcripts file using a custom reference gen...
• significant genes not shown in the scatter and volcano plots
  hello, When i plot the scatter plot and volcano plot for my cuffdiff output using cummeRbund it s...
• Cuffdiff significant genes
  I am new to RNA-seq analysis and wanted to know what is the best approach to filter out significa...
• Inconsistency Between Cufflinks And Cuffdiff. This Is Killing Me.
  <> The cufflinks and cuffdiff results are not consistent with each other. This is killing ...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• Running MACS2 without a control sample
  While going through the [Analysis of Chip-Seq][1] data tutorial, I realized that one of my input ...
• 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 Statistical Calculations Are Inconsistent?
  Hi, I'll preface my concern by saying that I'm a novice to Cufflinks. Back in September, I perfo...
• Controlling for batch effects in RNA-Seq data
  Hi, I was hoping that someone might be able to give me some advice on adjusting or controlling f...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• Error in CuffDiff
  I would be forever grateful if someone could take the time to help me. I am attempting to analyze...
• Help With Cuffdiff
  Hello, I am new to cuff diff and just got my data output back and it doesn't look like anything ...
• Identify Different Number Of Differential Expressed Genes Using Ensemble Or Reseq Gtf
  Hi all, I am analyzing significant differential expressed genes for a pair of normal V.S tumor, ...
• Using Cufflinks v. 2.2.1.5
  Hello community, Let me lead with, I have never been able to successfully run the tophat2-cuffli...