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• cufflink jobs in queue for 3 days
  Hello, I had set up a cufflink job saturday morning. I thought it may have been an error on my e...
• CuffLinks/Server Running for a VERY Long Time
  I am currently analyzing RNA-seq data and running cufflinks. I originally started the Job in earl...
• Cufflinks in galaxy
  When I am using cufflinks in galaxy the option use reference annotation, when selecting use refer...
• Problem With Running Cufflinks
  Hi everyone, After mapping my RNA-seq data to the reference transcriptome using Bowtie, I trie...
• Bias Correction : Locally cached human reference sequence data
  For a cufflinks run, Galaxy detected up human (homo Sapiens) hg19 for the locally cached referenc...
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• cufflinks not running
  I am trying to upload my data for cufflinks at usegalaxy,but its not runnng.kindly help
• Cufflinks on large files
  Hi all, I'm using Cufflinks from NGS:RNA analysis on a data set that's about 30gigs with the Ga...
• Gff3 not recognised by cufflinks
  I am trying to use cufflinks, but it does not recognise my reference annotation.  I have a gff3 f...
• Stranded vs unstranded cufflinks
  Dear Biostar, Im having issues with my RNAseq libraries. The library was made with the NexteraX...
• Cufflinks 0.0.7 and CummeRbound
  Hi All,   Has anyone had any experience with running R package CummeRbound with cufflinks veris...
• 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...
• Long wait times
  Hi, I understand there was a clustering issue this weekend and it has been resolved. I re-entere...
• Tool failure that reports: AttributeError: 'module' object has no attribute 'ICM'
  Hi, I want to run Tuxedo2 workflow associating cufflinks with a gtf annotation file. TopHat se...
• Workflow won't start running
  Hi, after assembling my own workflow and running it, I get the usual notification that it is run...
• cufflink trancript analysis
  Dear sir, i have run my cufflink analysis on friday but my job does not execute... please help me...
• RNA Analysis cufflinks
  How long does cufflinks usually take to run on RNA analysis? I had it running for about an hour a...
• Any Thing Wrong With My Cufflink Process In Galaxy?
  Dear all: Recently, I run cufflink in galaxy on the internet. I want to compare two samples, How...
• low number of assembled transcripts for cufflinks with annotated genome
  So I am pretty new to the bioinformatics movement and am having trouble assembling trancripts usi...
• Cufflink not running
  Dear galaxy admin and user, Cufflink is not running for two particular datasets. While cufflink ...
• 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...
• Can't auto detect metadata
  Hi, I ran Tophat on my RNAseq data and an error occurred setting the metadata. This has happened ...