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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...
• Cuffdiff: Same Gene Listed With Different Fpkm Values
  Dear all, has anything like this happened to you? I compared two samples with cuffdiff and when ...
• 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...
• Cuffdiff Fpkm=0 "Not Significant"
  Dear forum, whoever knows this please tell me!!!!! Given two fpkm . e.g. fpkm 1=2922828 and fpk...
• 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 ...
• Getting Figures from R with Galaxy DESEQ2 output?
  Hi, So this summer I ran a bioinformatics workflow on differential gene expression in three samp...
• fasta sequence from differential expressed gene
  Hi, I am Galaxy user. How could I get fasta sequences of differential expressed genes from Galaxy...
• 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 Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• Cuffdiff Results Missing
  Hi, I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group one has two replicates ...
• differential expression exon-level
  Hi everybody, I've been using cufflinks in order to perform differential expression between to g...
• How to analyse the gene expression matrix which I downloaded from GEO by Galaxy?
  I downloaded the gene expression matrix from the GEO, it is excel format. In this file, there are...
• Generation of reference using CLC Genomic Workbench
  Hello everyone,  I  have to analyse the transcriptome data in order to identify differentially e...
• differential expression ballgown pData
  Hi everyone, I am using ballgown to do differential gene expression analysis. But I have a questi...
• 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,...
• cummerbund tool error
  Hello, I recently tried differential gene expression analysis using an established workflow. I h...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Remove batch effects with galaxy
  Hello, I am having a problem with batch effects on my RNA sequencing data, where I try to determ...
• 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...
• How To Determine Differentially Expressed Genes Using Galaxy?
  Hi All, Could anyone tell *Which Version Galaxy* has the function to run DESeq (determine differ...
• How Much Fpkm Can Be Take Into Consideration When Compare Gene Expression
  Dear All, I am comparing the gene expression between two cell types by examining the Cufflink ou...
• How To Do An Go Enrichment Analysis In Galaxy?
  Hi everyone, I got a list of differentially expressed genes from my RNA-seq data. Is there a t...
• assembled transcripts TO BLAST2GO
  Hi , i want to compare the ontologies of genes generated from cuffdiff output and use it for BLA...
• Differentiate data between two heatmap data sets
  Hello, I had Bowtie mapping alignment file for each of my two ChIP-seq samples. Then, I did heatm...