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• cufflink and tophat queueing more than 24hrs
  cufflink queue is not working. I have been trying to run tophat and cufflink since last 2 days, n...
• Error Running Cufflinks On Galaxy
  Dear all, I tried to follow the Cufflinks tutorial created by Jeremy. The problems start with fi...
• cufflinks running problem
  Hello, I´m having problems in running Cufflinks. Yesterday morning I used the Tophat accepted hi...
• Need help with "Cufflinks" tool
      Tool name: Cufflinks Tool version: 0.0.7 Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/cuf...
• Cufflinks never start??
  I am still a newbie on Galaxy. I mapped my RNA-seq reads by TopHat without problem (I believe), ...
• Gene annotation dataset from Ensembl not recognized by Cufflinks
  Hello Galaxy/Biostars, I am trying to perform RNA-seq analysis using Cufflinks at Galaxy. In ord...
• Cufflinks Output In Ucsc Browser
  Hi all, I am doing cufflinks assembly of TopHat-aligned NGS reads with Refseq gene track as refe...
• Cuffmerge Error
  Hello, The problem is most likely with the SAM files and sorting. Please see: "Why won't my SAM ...
• galaxy problm cufflinks
  hi i m working on rna seq analysis.all my sam and bam files are more than 4 gb i upoaded it usi...
• Cufflinks Set Parameters
  Hi,   It's the first time for me to use cufflinks in galaxy, two choices confused me as follows: ...
• Usegalaxy main server down? (Queue not working) - PROBLEM FIXED
  Hi all, Is the main usegalaxy server running, or is it just under a high work load? I've run cuf...
• The cpu using question when I run the cufflinks.
    My question is, my "cufflinks" using the 100% cpu before the others run the "blastx", but no...
• No Cufflinks data
  Hello, I have been trying to use Cufflinks for my files from FasqToSam but I I have not been ab...
• Need help with "Cufflinks" tool
  Hi, How long does it take usually that GALAXY upgrade with a new version of Cufflink (version 2....
• cufflinks on Rna -seq data not working
  every time i am trying .. processing doesn't go along it stops.. After several time refreshing it...
• Cufflinks: reference annotation file for Nile Tilapia (Oreochromis_niloticus)
  I want to do differential gene expression analysis on some Nile Tilapia RNA-Seq data using the Cu...
• Hisat2 Cufflinks Cuffmerge cuffdiff problems
  Hello I am working with cufflinks programs but I have different problems. **1.-** Fist I used o...
• Cufflinks Reporting Fpkm Values Of All Zeroes (0)
  Hello! I have come across a problem where Cufflinks is reporting all FPKM values ...
• Cufflink not running
  Dear galaxy admin and user, Cufflink is not running for two particular datasets. While cufflink ...
• Cufflinks generated duplicated features
  Hi everyone i post my situation because i have this error: > GFF Error: duplicate/invalid 'tr...