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• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• Proximity Search
  Hi there. I am trying to find the genes that are within 10kb (in the upstream region of the gene)...
• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• Keep Alive for Communication Between Pulsar and Galaxy
  I have a linux server running the galaxy that needs to communicate to a windows machine using pul...
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• 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...
• Questions On Cuffdiff Output And Browser Visualization
  I would really appreciate someone's input on some issues I am having with my cuffdiff output for ...
• Issue With Saving 'Manipulate Fastq' In Workflow; And Request For Advice Dealing With Barcoded 454 Data
  Hi, I'm a new user, learning how to use Galaxy while I wait for my 454 results. So I'm not actua...
• VERY new to Galaxy: How do I query by row and keep rows with specific values
  Hi - I've been using Galaxy for about a week now on my own. I'm a total newcomer this world, so p...
• Counts per million to differential expression
  Hi All, Strange question so a bit of background: I have used a targeted RNAseq panel so it is e...
• Extract Data And New Genes
  Hi Everyone, I am working with *Aedes aegypti * and I obtained around 500 million reads (HiSe...
• VCF gene name sorting
  Hello, I have a vcf file and need to tie it to the gene name. I did this with the vcf annotate t...
• Faulty BAM/SAM files after Bowtie2, filtering and sorting
  Hi, I have some ChIP-seq data which I have aligned with Bowtie2 on Galaxy which gave me BAM file...
• [Genome] Genome-Wide Dataset Of Protein Location Conversion
  Hi Dana, the way I do it, is the following: Get a list of all genes (e.g. RefSeq) using the "Ge...
• Display data summary from R code in my galaxy tool
  I have created a galaxy tool, which get the gene expression data. I want to do some gene express...
• Critical Feedback
  This student was more adventurous. I think he actually could do more of what he tried with more e...
• htseq-count with gff error
  Dear all. Please take a look at my errors: http://goo.gl/Oa2IxR In the link, you will see 2 ima...
• fetch taxonomic representation question
  Dear Galaxy, I am getting strange results back when using Fetch Taxonomic Representation. When ...
• troubleshooting Get Data from local instance
  I've got a local Galaxy instance and I'm getting errors when I try to get USCS data.  The specifi...