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• Tophat vs Bowtie2
  Hello, I took the fasq files and ran Tophat then Bowtie2. Is it okay to run tophat first then bo...
• bowtie2 is stalled
  Hello! My bowtie2 runs have been in the queue for a full day. I've never seen it take this long. ...
• Queue status for bowtie2 run? Over 1 hr 15 min? Doing something wrong?
  Have had a single bowtie2 run on demo database running over an hour. Is this right? How can I get...
• Bowtie2 not running
  Hello, I have 4 Bowtie2 analyses that I executed about 18 hours ago that are still grey and queue...
• Tophat can't see the build-in reference genome?
  I successfully fetch an hg19 and build an bowtie2 index with Data managers. Bowtie2 can see the r...
• Bowtie2/BWA-MEM remain waiting to run for several days in Main server. Is it only in my account?
  Hi all, I've been trying to run Bowtie2 and BWA-MEM with several datasets and in different histo...
• Trying to run a Tophat on a local galaxy server but it gives me an empty bam file and following message: galaxy_27.sh: line 29: bowtie2-build: command not found
  I am trying to run a Tophat on a local galaxy server but it shows a following message. I guess I...
• No chicken reference genome (galGal4) for Bowtie2 - map reads against reference genome
  Hi, I cannot find the chicken (galGal4) reference genome when I run Bowtie2 - map reads against ...
• Bowtie2 not working
  Dear sir, i have uploaded some RNA Seq data and done with FastQc. I wanted to map the reads to m...
• bowtie2 output only mapped reads --no-unal option
  Hi, I've been trying to run the galaxy bowtie2 tool and couldn't find an option to report only a...
• Mapped paired-end reads with Bowtie2
  Hi Biostar community, I have paired-end reads for MeDIP-seq. I'm able to mapped read1 and read2 ...
• Bowtie2 jobs queued for over 24hours
  Hi, Are there currently any known issues with bowtie2? I've had a couple of jobs that were queue...
• Problems running Bowtie2!
  Hi everyone, I'm trying to map a paired-end seq. to the human genome using Bowtie2. Unfortunately...
• error long spanning reads Malformed
  Hi, I have ran the Tophat 2.08 version and I have obtained this "result".log [2014-09-10 09:47:...
• Bowtie 2 error
  Hello. I am trying to run bowtie2. This is directly from the Biostarhanbook. Get reference: ACC...
• Where to find Bowtie2 output stderr filehandle?
  Dear all, I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") ...
• Paired-end dataset collection with Bowtie2
  Hi, I made a paired-end fastqsanger dataset collection and tried to run it with Bowtie2, but it ...
• Bowtie2 samples are not queueing
  Hello, I ran bowtie2 last week June 16th 2017 and two of my samples have had trouble running thr...
• Error running BWA-MEM or Bowtie2 in usegalaxy
  Hi, I am getting following errors while trying to run BWA-MEM or bowtie2 in usegalaxy. The input...
• Bowtie2 samples still in queue after 48 hours
  Hello, I am currently using Bowtie2 and my samples. 5 out of the 6 ran but one has been in the q...
• Error occuring in CleanSam after alignment with Bowtie2
  Hi, I am just starting to get familiar with Galaxy and bumped into a problem of which I don’t kn...