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• Problem Mapping 454 Reads In Fastq Format Using Lastz
  Dear Galaxy Team and users, I have some 454 reads that I would like to map against a contig asse...
• TopHat: Error: Couldn't build bowtie index with err = 1
  Hi I'm trying to run TopHat on a Cloudman Galaxy instance and I keep getting the below error. I'...
• MACS returns an error
  Hi again! I am trying to run MACS on my treatment and control, but it comes back with an error. I...
• [Fwd: Re: Error Occurred When Converting The Solid Output To Fastq]
  Subject: Re: [galaxy-user] error occurred when converting the SOLID output to fastq Date: Wed,...
• GATK (deprecated tools)
  **Objective** The objective is to implement a variant discovery and annotation pipeline similar ...
• TOPHAT error: segment-based junction search failed with err =-6 what(): std::bad_alloc
  Anyone know what this error is about or how to troubleshoot? Most samples work fine, but some thr...
• Galaxy cloud instance won't initialize
  Hi Galaxy Team,   I am in desperate need of using the cloud so that I can analyze by rather lar...
• Archived cloud- Cloudman
  Dear all, I'd be grateful for help with the following issue. I recently did a big RNAseq analysis...
• 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:...
• 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...
• galaxy start error
  I installed a local galaxy and start it successfully. Then I'd like to add some pipelines into m...
• How Should I Include Biological Replicates In Cufflink/Cuffdiff?
  Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcripto...
• Problem With Scientific Notation Sorting And Filtering In Galaxy
  I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered ...
• Problems adding bulid-in genomes for tophat on local galaxy
  Hi, I have a question regarding tophat2. I would like to add some mammalian genomes to run toph...
• GALAXY_SLOTS and slashes
  Here is my experience with an exercise to make Galaxy utilize a multi-core / multi-processor envi...
• Install-tools via yaml file error
  dear all, I want to install a bunch of tools using the install-tools function. In my yaml file to...
• Galaxy PBS system
  I am currently setting up a PBS system to work with Galaxy. When submitting a job I see the foll...
• MACS giving result for inout data but error in Test data
  Hello , I am facing problem when I am trying to use MACS . It is giving data for input data but w...
• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• Galaxy Community Conference Early Registration Deadline Extended To May 1
  Hello all, The early registration deadline for the 2011 Galaxy Community Conference has been ext...
• Freebayes on Galaxy shows vcf output with GT INFO field as 0/0
  Freebayes on Galaxy shows vcf output with GT INFO field as 0/0. Chr1 10000171 . G A 6.18434e...
• 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...