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• Empty Cuffdiff Output
  What does empty Cuffdiff FRPKM empty files means? I was not able to run my RStudio for my Cuffdif...
• CUFFDIFF BLAST2GO
  Hi, I want to use my cuffdiff out for BLAST2GO in Galaxy, kindly advise how can i configure cuff...
• problem in visualizing cuffdiff data
  I got result for cuffdiff in galaxy, but iam trying to visualize the output using CummRbund it sh...
• CuffDiff is no more in the list of NGS:RNA-seq
  I cannot see anymore CuffDiff in the list opening NGS:RNA-seq. I need to use it. Help
• Cuffdiff analysis output
  Hi there, I tried to run cuffdiff with the annotation of iGenome but still no sucess to have a o...
• CummeRbund input from Cuffdiff output
  Hello All I just finished my Cuffdiff on a set of practice data, and I am planning to visualize...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...
• 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...
• 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 ...
• question about the cuffdiff setting
  Dear Sir/Madam, I need to know what is the differance between the Geometric, Classic-fpkm and qu...
• Hidata
  After running Cuffdiff, I got more than 95% of genes with HIDATA status. What should I do?
• can not visualization
  hi, I have finished cuffdiff, and want to visualize the result. But  I can not add datasets to vi...
• Tarcking ID in cuffnorm output and TestID (geneID) in cuffdiff output, are they the same?
  Dear all, I found in the output of cuffnorm there was no locus information corresponding to my d...
• How to get all possible group pairings in cuffdiff- Main
  Hi, I have 4 samples and followed the tophat, cufflinks, cuffmerge and cuffdiff workflow.  I mer...
• 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...
• Cuffdiff taking forever on AWS
  I have been running Cuffdiff for ~36 hours on a two condition comparison... And it is not finishi...
• 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...
• Cummerbund - Biological Replicates Problem
  Dear all, I would like to visualise by CummeRbund the Cuffdiff results obtained using the cuffli...
• Galaxy With Cuffdiff Output
  Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc...
• Cuffdiff gene name
  Hi! I am analyzing RNA-seq using tophat-cufflinks-cuffdiff, but at the end, in the cuffdiff tabl...
• How to use cuffmerge and cuffdiff
  I am trying use Galaxy to analysis the yeast RNA-seq data. When I want to try the cuffmerge and c...
• zero cuffdiff FPKM values SusScrofa
  Good morning, I am a beginner in RNAseq Galaxy interface and I have a problem with all zero FPKM...
• Cuffdiff Errors
  Hello, I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 sampl...