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• Cummerbund visualization of expression plot
  I am following the NGS101-16 video on Cuffdiff/Cummerbund to learn how to use Cummerbund. For ex...
• How To Extrapolate Differentially Expressed Genes After Running Cuffdiff?
  Hi guys, have a question about the cuffdiff output "differential expression testing". For most o...
• 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...
• comparisson of RNA-seq FPKMs across samples
  Dear BioStars community, I am trying to "recycle" some RNA-seq data published as supplementary m...
• Replicate Common Gene Names
  This is somewhat Galaxy related, but more of a general question. I did all of my mapping and ini...
• cufdiff output-cutoff pvalue and parameters for differential expression
  dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run...
• Help for pathway image: draw a KEGG pathway
  Hi, I have a list of genes generated from ucsc genome browser and output directly to Galaxy. I t...
• 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...
• Differential expression from FPKM
  Greetings, I've been using some of galaxy tools for the last months, namely for tuxedo pipeline. ...
• RNA-seq analysis for a small number of genes
  Hi all, I am new to RNA seq analysis and want to look at the expression of a small number of gen...
• Cuffdiff Results Interpretation: High Fold Change But Not Significant
  Dear team, I've been having some problem with cuffdiff results interpretation. I understand that...
• Rna-Seq Cds, Splicing And Tss Fails
  Hi all, So I am using cuffdiff to find significant differences between two samples (no replicat...
• How do I obtain gene names from ENSG values?
  Hi I have performed DGE using DESEQ2 (input htseq-count, following mapping by BWA-MEM) and have ...
• Sorting ChIP-Seq peaks
  Once I have ChIP-Seq peaks from MACS, I am wondering if there is an easy to sort the peaks accord...
• 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...
• Inconsistent Cuffdiff
  dear all these are the cuffdiff outputs for the same transcript/gene (one isoform only): transcr...
• Display data summary from R code in my galaxy tool
  I have created a galaxy tool, which get the gene expression data. I want to do some gene express...
• Suggestion To Change Cuffdiff -C "Min Alignment Count" Default To Author'S Value Of '10'
  Hi Galaxy Developers, This is regarding the wrapper for cuffdiff and the -c parameter for "Min...
• Cufflinks Quartile Normalization
  Can someone help me understanding the quartile normalization in Cufflinks? I read different threa...
• 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 ...
• Counting number of times multiple defined values appear in the dataset
  I have gotten SNP data on a number of regions via UCSC genome browser. I have assigned all SNPs w...
• How Insert Gene Ids?
  Hi, I have used the RNAseq tools to calculate the FPKMs values, now I would like to know how I c...