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• How to use cummeRbund to draw plots after processing cuffdiff? (cuffdiff does not output .sqlite file as it should)
  Hello, I created a workflow having Cuffdiff in the end, which outputs the last file, .sqlite fil...
• cummeRbund SQLite database error from Galaxy main CuffDiff tool
  I'm trying to create an SQLite database to download and use with cummeRbund by using the "Create ...
• Analysis of Galaxy Cuffdiff output by CummeRbund
  Hi, I am trying to use cummeRbund in Rstudio to analyse my Galaxy Cuffdiff output. However I am ...
• Cuffdiff input into Cummerbund error?
  Hi all, So I completed a standard workflow using top hat through cuffdiff in order to find diffe...
• not able to use cufflinks output from galaxy in cummeRbund
  I am using online galaxy server for rnaseq differential analysis. I am not able to use cufflinkou...
• Galaxy Cuffdiff output doesnt correspont the output from manual
  Hi people! I was trying to run the local version of cummeRbund but the files that I get from the ...
• Reference Genome unable to be detected on cuffdiff/cufflinks & Empty CuffDiff output files
  Hi, I am currently following the tophat->cufflinks->cuffmerge->cuffdiff pipeline. Every...
• Generate SQ Lite database for cummeRbund not working with CuffDiff, and other general questions
  Hi everyone, I am currently a final year undergraduate studying at UoM set with the final yet pr...
• problem in visualizing cuffdiff data
  I got result for cuffdiff in galaxy, but iam trying to visualize the output using CummRbund it sh...
• Has anyone successfully run CummeRbund in Galaxy?- Gene ID Null
  I am struggling with the final steps of my RNA-Seq pipeline. The data has been cleaned up, mapped...
• Cuffdiff analysis output
  Hi there, I tried to run cuffdiff with the annotation of iGenome but still no sucess to have a o...
• Can standard CuffDiff output be used as input into CummeRbund on Galaxy?
  I've been analysing some RNA-seq data in triplicate and I want to compare replicates by generatin...
• Extract-Cuffdiff & Plot-Cuffdiff tools missing in NGS:RNAseq
  Hi, I was testing the new Cuffdiff implementation in Galaxy and I produced a Cuffdiff output in ...
• Cuffdiff crashed if I try to use option "Generate SQLite"
  I am running Cuffdiff on my data, It runs fine, but if I am adding option "Generate SQLite" it c...
• Cuffdiff output_version 2.2.1.1
  It seems that the new version of the cuffdiff tool on the main galaxy mirror outputs an sqlite da...
• create sqlite from cuffdiff terminal
  if there is a way to put an option when you run cuffdiff from terminal so that you can get an sql...
• 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...
• Cuffdiff not working in Galaxy
  Hi, I'm trying to run cuffdiff as part of an RNA-seq project, and it's not working. I've tried l...
• Tabular to Excel
  Hi there, I have a cuffdiff output in a TABULAR format file and I'd like to convert it to an exce...
• Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
  Hi! I ran into a problem using Cuffdiff. (I am using a local version of galaxy). When I try to ...