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• How to make multiple Tophats inside a workflow to run sequentially rather than simultaneously?
  In my workflow on Galaxy, I have 6 fastq samples to run through Tophats and their output bam fil...
• Tophat taking too much time
  Is this a server error or data size overload?? Tophat is still running since long time. I got res...
• Tophat not working?
  I have been trying to run Tophat for days. The jobs just keep sitting in the queue. I thought it ...
• 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 job running for two days
  Hello, My Tophat job has been running for two days not. In the meantime I just completed an aut...
• Need help with "Tophat for Illumina" tool
  Dear All, Hello amazing Galaxy team members  now i have 14 manipulated fastq files 7 forward an...
• 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...
• Tophat not executing
  Tophat doesn't seem to be executing on usegalaxy.org. The jobs are being queued, but they haven't...
• TopHat is not running
  Hi, I uploaded TopHat jobs from last Friday and it hasn't start running yet. Is there a proble...
• How to run multiple threads in Tophat and Cuffdiff on Galaxy?
  I want to run multiple threads in Tophat and Cuffdiff on Galaxy (“-p” option). But in the tool f...
• cufflinks running problem
  Hello, I´m having problems in running Cufflinks. Yesterday morning I used the Tophat accepted hi...
• TopHat: Raw junction and juncs files
  Hi I'm having a hard time finding information on what exactly the advantage of using the Raw Jun...
• TopHat from Galaxy local instance do not recognize available fastq files.
  Hi there, I am probably missing something obvious here. My local Galaxy TopHat does not recogniz...
• TOPHAT ERROR tool execution
  Hi,   i tried running my datasets and tophat gives  error all the time.  Thanks
• Tophat jobs waiting 48hrs
  Hi, I have had a number of Tophat jobs queued for 48hrs now. Is there a long waiting time right ...
• Tophat vs Bowtie2
  Hello, I took the fasq files and ran Tophat then Bowtie2. Is it okay to run tophat first then bo...
• Error message in Tophat
  I am receiving the message "an error occurred setting the metadata for this dataset" on all jobs ...
• Tophat is not provided anymore?
  I don't see Tophat in galaxy. I wonder if it is no longer available or it is just temporary. Can ...
• tophat failure job
  i have run fastqgroomer again on the sra sequences and waiting for it to complete. its result i p...
• Tophat
  Hello, I am a new galaxy user, still trying to find my way around. Is there a way to run Tophat ...
• TopHat Not running
  Is TopHat not running again? I have jobs that won't start over 24 hours and keep showing it is wa...
• Bam File After Tophat Run
  I am running RNAseq in Galaxy after running Tophat I am trying to save Bam file but by default it...
• Running TopHat locally
  Hi, I'm trying to run Tophat2 on a local instance of galaxy. Tophat2 and Bowtie 2 have been inst...