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• Bowtie mapping result
  Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference ge...
• How to contact Galaxy Team re: BWA, bowtie if your genome of interest is not listed..
  I'm interested in using Galaxy for my project - while the Rhesus macaque genome is included in bo...
• Bowtie don't load paired end data
  Hi, I'm new in the NGS technology. I have a problem with Bowtie paired end loading data. A few we...
• why Tophat very very slow on the galaxy project last 2 days?
  Hi everybody, I was using Tophat last week it was a little bit fast, now I'm trying to run a job ...
• 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...
• Problems running Bowtie2!
  Hi everyone, I'm trying to map a paired-end seq. to the human genome using Bowtie2. Unfortunately...
• Built-in indexes not working in Local Galaxy Instance
  Hi, I've just finished setting up a local Galaxy instance and everything works fine except for b...
• Changing Bowtie Parameters In Tophat
  My apologies if this has been covered before but I am using Galaxy Main and wonder if, when runni...
• Bowtie not working
  Hi I was trying to map with Bowtie last night and this morning but the run failed as soon as it s...
• Need help with "Map with BWA for Illumina" tool
  Hi,  I've been mapping this sample many times without any problem.  Now I'm trying to do the ex...
• Workflow is not initiating a job in my history
  Hi All, I'm trying to use a a workflow to do the last two steps of my analysis (map with bowtie ...
• disk quota is low
  Hello, While RNA-seq data have been running, the sign came 'You are over your disk quota. Tool e...
• Problems with Bowtie 2
  Is there a problem using bowtie 2 since 1200 yesterday. None of my jobs submitted since yesterday...
• Making a Temporary Directory in an XML File
  Hi all. I'm making a custom bowtie tool, because the current bowtie tool only accepts FASTQ files...
• Recent problems writing Bigwig from Bam files
  I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A ...
• ChIP seq : How to map sequencing data that one base is not called?
  I did ChIP-sequencing. During sequencing process, one base was not called due to a problem at the...
• Collapsing and Mapping Reads
  Hello, I'm starting with FASTQ files and want to Collapse the sequences and then Map them to the...
• mapping tools error: "Remote job server indicated a problem running or monitoring this job"
  Hi, I'm trying to use bwa or bowtie to align paired collection of reads. However, I am continual...
• Cufflinks Returned 0 Value In All Rpkms
  Hi I have been trying to analyze a rat Solid SRA but I encountered a problem: cufflinks gave me ...
• Macs
  while using MSCS tool from Galaxy I get following mesg. with BED file: "Treatment tags and Contr...
• Problem With Bowtie
  Hello, I am completely new to using galaxy. I have a quick question. I have uploaded my fastq fil...