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• After 'Trim Sequences', 'Map W/Bowtie' Job Has Been Waiting For Days To Run
  Greetings, I am using Galaxy Main; On 8/1/2013, and after 'trimming sequences' on my 'FASTQ groom...
• Help: Mapping With Bowtie Does Not Start
  Hello, I am trying to map sequences with Bowtie for Illumina. I have been waiting for a whole d...
• Job waiting to run
  To whom it may concern,   I am trying to run a bowtie with Illumina, but I have been waiting fo...
• Bowtie Alignment
  Hello, I am trying to map my Illumina reads to the mouse genome using specific Bowtie criteria. ...
• Prolonged - Job Waiting To Run
  Dear Galaxy team,   I am running short read alignments with Bowtie for illumina using some data g...
• Mapping Does Not Start
  Hi, I am trying to map sequences with Bowtie. Have been waiting for a few hours now but it still...
• Need help with "Map with BWA for Illumina" tool
  Thanks a lot for your answer. I  used FASTQ groomer to convert fastq format to fastqsanger. I sta...
• Unicycler job has been waiting since Monday evening (11/27/2017). Am I doing anything incorrectly?
  So I have uploaded my sequence data as of Monday evening, as the title says, but the job has been...
• Bowtie mapping result
  Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference ge...
• Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
  Dear all, My problem seems like something that should have a very simple solution from my end and...
• Map with Bowtie for Illumina
  Hello, I created an NGS mapping job over Galaxy today at 18:45. Is it normal that it is still in...
• Every job is waiting to run
  I wanted to upload mu trimmed reads to galaxy and map them using bowtie, but the only task I was ...
• 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...
• Help W Sam To Bam
  Hi, We're loving Galaxy. This is an excellent interface and set of tools. The issue we're havi...
• Bowtie Mapping Waiting To Run For 3 Days
  Hi, I was wondering if I have to re-run them or if I just need to wait. Thanks, Yanina
• Job starts running then is resubmitted and queued
  Hi, I have submitted multiple jobs to both Bowtie2 and Bowtie for Illumina, and although 2 of th...
• Job is waiting to run.
  Hello,  I have been trying to run a Bowtie job(s) for two full days and they just hang with the ...
• Tophat Error: Segment-Based Junction Search Failed With Err
  Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, so...
• Bowtie
  Hi Experts, I have single end Illumina reads from ChIP-Seq experiment. The files have encoding I...
• Tophat Error: Segment-Based Junction Search Failed With Err
  Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this er...
• Job waiting to run
  Hi,   I used Cufflink to run some jobs. It's been quiet some time but all my jobs are still wai...
• Bowtie trouble for aligning small RNA reads
  Hi there, I’ve been trying to use Bowtie to align my small RNA NGS reads (fastq groomed, for San...
• Re: Output File For Bowtie Suppressed Reads (-M/--Max)
  Hi all, I'm running into a problem with the output from bowtie mapping for illumina reads. I'v...