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• Can't use Tophat on Galaxy.
  Hi,  I am having difficulty figuring out the Tophat tool on Galaxy. I was trying to use the Toph...
• Is there a way to fetch taxonomic information for a list of GI numbers in Galaxy?
  Hello, I performed a MEGABLAST analysis a few days ago, but I am now unable to automatically ret...
• no fastq data set available
  Hi, New to this program. Have my files uploaded in the history and have also made a dataset. How...
• Filtering Pile-Up Fails
  Dear All, I have been successful by using the online tool to align Illumina pair end reads , eac...
• localhost workflow problems
  hi all,  I've been trying to use the workflow in galaxy workflow, but it seems like that I can't...
• no fast groomer on galaxy (Mississippi server)
  Hi,   I need to convert fastq files to fastqsanger before mapping with Tophat but I'm working o...
• Re: Getting Reference Index Files In Local Galaxy Install
  Hi, We have a local install of galaxy and I'm trying to add the reference index files for bwa usi...
• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• bwa not recognizing fastq files
  I am trying to map a set of fastq sequences to a custom genome, using BWA. The two setrs of trip...
• Where can I find the FastQC tool on the Galaxy webpage?
  Hi,  I am attempting to recreate an RNA Seq differential expression analysis of a previously pub...
• trimming illumina single end DNA seq
  Hello, I am trying to trim a single ended  DNAseq by using Trimmomatic tool. But "Input fastQ fi...
• Private vs Public Galaxy: different outcomes following Fastq upload
  We are experimenting with setting up our own cloud-based Galaxy server using the Cloudman tools a...
• Fastq Joiner
  I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joine...
• Fastqsanger to FastQ
  I am trying to run a utility called transrate to assess my trinity assembled files. I am trying t...
• 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...
• Mapping With Tophat Vs. Bwa
  Hello, I am getting what seems to me to be strange results using two different mapping tools in ...
• Need help with "FASTQ splitter" tool
  I was having difficulty with the FASTQ splitter, it was not finding my fastq file (an SRA-based F...