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• Critical Feedback
  This student was more adventurous. I think he actually could do more of what he tried with more e...
• How to intersect vcf files for commonly mutated genes only (not the exact mutation)
  Hi all, I intersected two vcf files using vcf-vcf intersect on usegalaxy.org and I realized that...
• How to filter genome annotation results to get a report focused on specific gene mutations (positions)?
  How to filter genome annotation results to get a report focused on specific gene mutations (posi...
• Raw Count Of Genes
  Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-inf...
• RefSeq Annotation using SnpEff
  Hello, I am working with human whole genome sequence. I have called variant using samtools and I...
• Zygosity of mutations
  Hi all, While performing an analysis of NGS data I am not getting the column for mutation zygosit...
• 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...
• 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...
• Need help with "SnpEff" tool
  Hi there, I'm trying to run SnpEff on Galaxy, but the only Genome that it gives me access to is ...
• How To Find Out Snps And Point Mutations In Rna-Seq Data Using Galaxy?
  HI, I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy s...
• No tab named cloud on my version of galaxy
  I have no tab "cloud" on my account in order to login to cloud launch of galaxy at AWS. How can I...
• Running SnpEff on Galaxy
  Hello, I would like to annotate a .vcf file and also summarize possible effects variants can hav...
• SnpEff output searching for specific genes
  Hi, I have successfully runned SnpEff. The ouput VCF file contains 2.5 million "lines", data set...
• BAM tool?? tab-delimited, coordinate sorted output file - displays calls, depth at every coordinate?
  I'm trying to figure out how to create a tab-delimited, coordinate sorted, file type that display...
• Variant Annotation In Galaxy
  Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genome...
• On executing SnpEff n a Galaxy cloud instance we have the error: All frames are zero
  On executing SnpEff we have the following error: WARNING: All frames are zero! This seems rather...
• trinity statistical analysis
  Hi I am new trinity user at usegalaxy. I used trinity to assemble my NGS data and received fasta ...
• Where can I find the Trinity statistics?
  Hi, This is maybe a stupid question, but I am new to RNA sequencing and the Galaxy environment -...
• computeMatrix skipping bug is causing a problem with large data sets
  When running computeMatrix with a large set of data I keep receiving this error multiple times ea...
• 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 ...
• BRCA1, BRCA2 mutation detection in galaxy
  Hello all. I am beginner Galaxy.^^ Question : I want to know. Can I analyze some mutations o...