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• 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...
• simple qu: amalgamate and/or transpose mutational and clinical data
  Hi Probably a beginners question for most of you so apologies! I have excel spreadsheet of 400+...
• Exome Seq Work Flow
  I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotatin...
• Analyzing somatic mutations from TCGA's level 2
  Hi, there! To make it short, HOW CAN I ANALYZE EXOME-SEQ DATA FROM TCGA PORTAL? I have downloade...
• How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud?
  How to get a .tab file with a list of mutated genes out of SNPEff in Galaxy cloud statistic HTML ...
• RNA-Seq analysis for 2 genes
  Hi, I did RNA-seq for 20 samples and I am interested in the differential expression of normal tra...
• Zygosity of mutations
  Hi all, While performing an analysis of NGS data I am not getting the column for mutation zygosit...
• Fwd: Hcc Mutations Workflow On Local Galaxy Instance
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• Hcc Mutations Workflow On Local Galaxy Instance
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• cDNA sequencing data analysis
  I am new to galaxy and sequencing data analysis. I have RAW files from cDNA sequencing and I am l...
• Rna-Seq Mutation Detection
  Hi,   I am trying to look at differences between two RNA-seq samples to see if there are mutation...
• Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
  Hello, Is there a galaxy package which will convert a .vcf to a .maf (mutation annotation file)?...
• NGS: Variant identification at specific positions in an enzyme engineering approach
  Hi, I am wondering how to extract the data of my NGS analysis. In my experience, I did site-dire...
• Extract/analyze base quality scores of mutations from BAM alignment
  Hello, I have RNAseq data aligned to my reference genome in BAM format. I would like to correlat...
• 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...
• Which tools can be used for gene annotation and for determining zygosity?
  I am unable to find VCFannotate tool in Galaxy and if I am using AnnovarAnnotate I am only gettin...
• 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...
• FASTQ quality trimmer
  I had a mutant and wild type FASTQ data of a mutant yeast strain. How can I perform FASTQ quality...
• Intersect more than two vcf files
  Hi everyone, I have nine vcf files that I'd like to intersect. I want to know which, if any, gen...
• Variant analysis using Galaxy - tutorials, example workflows
  I have my FASTQ files, and I am trying to align them to the mouse reference genome, and perform v...
• False negative results in GATK unified genotyper output
  Hi all, I'm having some problems with the output of the GATK unified genotyper.  Essentially I ...