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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...
• Tophat is stuck in "jobs waiting to run"
  Just had a quick question: I'm trying to use tophat, but my jobs are stuck in waiting to run. The...
• TopHat waiting to run issues
  Hello. I've been trying to run TopHat analysis on a dataset for over a week, it keeps getting st...
• Jobs (Tophat/cufflinks) waiting to load for several days (don't seem to be queued yet)
  Hello, I'm running tophat/cufflinks/cuffdiff on Galaxy for what seems like is probably a large d...
• Is there an issue or just longer than normal wait times..?
  Afternoon all, We've been waiting on some mapping (TopHat) for around 4 hours now and the job is...
• galaxy job waiting time
  Hello What is the waiting time for the jobs that were assigned. I have assigned a job with cuffl...
• Tophat jobs waiting 48hrs
  Hi, I have had a number of Tophat jobs queued for 48hrs now. Is there a long waiting time right ...
• Cufflinks and inner mean distance
  Greetings, I am attempting to use Cufflinks on alignments produced by running Tophat on some pa...
• Long wait time for Tophat
  I have a few RNAseq samples running TopHat for over 3 days now. I was wondering if you guys have ...
• Grey box with exclamation mark
  Dear Galaxy, I left the software running for 5 days doing a cufflinks job on some TopHat RNA seq...
• Tophat output Bam file
  Dear Sir, Tophat output bam file couldn't be downloadable there is an error showing this "usegal...
• Select Tophat And Cufflinks
  Hi,   I'm a user of galaxy.As I know, when TopHat and Cufflinks are supported through Galaxy, its...
• Jobs In Queue
  I have similar problems. My tophat job was sent 6 hours ago. Now the job is still waiting to be ...
• TopHat Not running
  Is TopHat not running again? I have jobs that won't start over 24 hours and keep showing it is wa...
• Re: Running Cufflinks On A Genome Without A Bowtie Index
  Noa, Using your FASTA in Tophat and Cufflinks is the correct approach. You don't need to provide...
• cufflinks running problem
  Hello, I´m having problems in running Cufflinks. Yesterday morning I used the Tophat accepted hi...
• Galaxy Cloud EC2 Response Error
  Good Afternoon I'm seeing this cluster error over and over today: 20:23:57 - Adding 1 on-dema...
• Tophat vs HISAT
  Hi, I've been using Tophat to align RNA-seq reads followed by Cufflinks to estimate FPKM. Now tha...
• Tophat job running for two days
  Hello, My Tophat job has been running for two days not. In the meantime I just completed an aut...
• mapping requests did not complete for many even with small file sizes (1-15 Mb).
  Hi Sir; I am new user for Galaxy.  I submitted files for mapping using bowtie and tophat.  Curre...
• Local Galaxy job delays: This job is waiting to run
  Hi, I have been trying to run job(s) for all the day on Galaxy and they just hang with the "wait...
• Galaxy Tophat for Illumina cannot be run, how to set parameters for Tophat for Illumina
  Tophat for Illumina cannot be run and is always 'This job is waiting to run' for three days, is i...
• How to find and extract novel transcript from cufflink and cuffdiff.
  I am analyzing Arabidopsis Rnaseq data. I was running Tophat and cufflinks, but after that I don'...