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• Cuffdiff Failed
  Hi, I had 3 samples (2replicates treated (A-B) and one untreated (C) ). I did cufflnks and cuff...
• Cufflinks Error With Illumina Igenome .Gtf For Annnotation
  Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcri...
• Cuffmerge fails to merge gtf files
  Hello, I am trying to merged to assembled transcripts produced by cufflinks using cuffmerge. I ...
• Cuffmerge error - how to fix it
  Hi guys, I am doing cuffmerge with reference annotation on my files after cufflink. The error oc...
• Cuffdiff Errors
  Hello I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 of my con...
• What is the purpose of Cufflink and Cuffmerge?
  Hi guys, I am new to the galaxy server, and I want to analyse my RNA-seq data with the following...
• Cuffcompare Or Cuffmerge
  Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experim...
• Problem With Running Cufflinks
  Hi everyone, After mapping my RNA-seq data to the reference transcriptome using Bowtie, I trie...
• Extract Genomic DNA error with custom genome
  Hi, I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to f...
• Cuffmerge
  I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guid...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Cuffmerge Error: Duplicate Gff Id Encountered
  Hello, I was doing a RNA analyse and I wished to compare the transcription and expression of two ...
• Solution For: Error Running Cuffdiff. Error: Cannot Open Reference Gtf File Condition, Control For Reading
  Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I th...
• Galaxy Tool Error Report From Johnwu@Ibms.Sinica.Edu.Tw
  GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the serv...
• Problems with Cufflinks 2.2.1.0 on local instance
  I have installed the latest version of Cufflinks on my local instance of Galaxy. Whenever I run t...
• Cuffdiff problems as part of a tutorial
  Hello, I have a problem with Cuffdiff, having successfully executed Tophat, Cufflink and Cuffmer...
• Sam Filtering And Header/Sorting Issues
  Dear All, I would like to add some filtering steps in my RNA-Seq pipeline. To do so, I used the a...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• Galaxy RSEM error
  Dear all,   I am trying to run RSEM via Galaxy but there is a problem. FYI, 1. Reference sequ...
• blast2go ontologies comparison
  Hi, i posted this question earlier also but received no feedback, kindly help.   I want to com...
• Empty data result from Cufflinks
  Hi I am trying to run Cufflinks on some BAM files that I have generated using HISAT2 with upload...
• How to resolve Cufflinks Fatal error: Matched on ERROR
  Hi, I've been running some RNA-seq analysis jobs on the Galaxy test server with PapAnu2 built-in ...