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• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Add stacks to galaxy
  I need to work with stacks to do analyzing my data. I downloaded version of stacks I needed but H...
• difference between $REPOSITORY_INSTALL_DIR and $INSTALL_DIR
  I wrote a tool for Galaxy and now I want to upload it to Toolshed. I am writing tool_dependencies...
• Stacks on usegalaxy
  Newbie question (I've only just started exploring Galaxy and so far it's great): I've come acro...
• Problems with STACKs in
  Sorry for bothering you, but I have encountered some difficulties in using STACKS at galaxy (loca...
• Difference between mRNA, CDS, transcript and gene in annotation file
  Hi, I am new to bioinformatics and have a very basic question. In the annotation files (gff) ava...
• Tool For Changes In Bedgraph Files
  Hi everyone, I am new to Galaxy and wondering if anyone can help me with a quick question. I hav...
• Demultiplexing reads with Stacks plus GTN tutorials with example methods
  Hello, i would like to demultiplex reads in FastQ format file, but i don't find "stacks" tool to ...
• Galaxy 101 Tutorial UCSC Browser version
  Hi there, Not sure which version of UCSC Genome Browser was used for the Galaxy 101 Tutorial. I ...
• Hitsat2: Spliced alignment options
  Hi, I am trying to analyze RNAseq data with HISAT2. I would like to include spliced alignment. I...
• Stacks in Galaxy
  Is Stacks still an application in Galaxy for analyzing Radseq data? I couldn't find it among othe...
• 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...
• New Software Needed
  Hi Jenn, I am working on RAD-sequencing. Two available softwares for analyzing RAD tags are Stac...
• "Get galaxy" site on my computer different from video in Module 5
  When I followed the video from Module 5 "Installing Galaxy Locally" the site I see is very differ...
• Finding Snp Differences Between Datasets
  Hi, I am trying to find SNPs and/or indel variants that differ between two groups of samples. Th...
• difference between tophat2 and tophat for illumina
  Hi  I have paired end read and am confused i should tophat 2 or tophat for illumina. What is the...
• Difference between Fastq and Fastqsanger?
  Hi,  Can somebody briefly explain the difference between fastq and fastqsanger files in Galaxy? ...
• Cuffdiff output redundant genes
  Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "...
• Rna-Seq Mutation Detection
  Hi,   I am trying to look at differences between two RNA-seq samples to see if there are mutation...
• Circle versus square
  Hello, I was just curious what the difference is between the loading circle and the loading squ...
• Mapping With Tophat Vs. Bwa
  Hello, I am getting what seems to me to be strange results using two different mapping tools in ...