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• DE NOVO TRANSCRIPTOME AND COUNT
  Hi,   I used STAR to assemble contigs for de novo transcriptomics data and used the following p...
• htseq read counts zero
  Hi, I have imported some fastq files (homo sapiens) from http://www.ebi.ac.uk/ena/data/ to Galax...
• Chip-Seq Normalization To Total Number Of Reads
  Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datase...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Re: [Galaxy-Bugs] Gi Errors In The Megablast Table Of Results ?
  Dear Sandrine, Thanks for pointing out this issue. The BLAST databases we have on Galaxy are fro...
• Filter by Evalue
  Hi I am using use.galaxy for analysing my blast data. I wanted to select contigs with evalue les...
• Comparing the Single and Paired End Assemblies
  Hello there!   Im using this touorial to analyze and assembly mate pair NGS reads for my illumi...
• Primer Contamination, Miranalyzer
  Hi Galaxy, Ive got 2 problems for you; 1) Ive got microRNA Illumina NGS data that I want to ana...
• SSPACE scaffolder: -m parameter limited to 50
  Hello, I am trying to scaffold my contigs after using the Velvet Optimiser in Galaxy (Orione CRS...
• Counts Of Mapped Reads For Each Gene?
  Hi Jen and other galaxy-users, I am analyzing our RNA-seq data. First, I mapped the RNA-seq da...
• using mPileup to examine allelic imbalance in hybrids
  Hi, I have some RNA-seq data for two different species and their hybrids. I want to look at the ...
• Correct way of merging samples for father, mother, child trio variant calling
  I am new to NGS data analysis and I'm working in a multiple-sample variant calling workflow. I ha...
• ERROR MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version - Eval Variant Tool
  Hi, I am getting this error when running eval variant tool from GATK ver 2.8 in galaxy. ERROR...
• Using BWA with Illumina data and metagenomic "reference genome"
  Hi, I'd like to try using BWA to align Illumina reads to some contigs a collaborator made from my...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Scaffold from Blast results
   Hi All I have been struggling to get my head around how to create Scaffolds. I have created a d...
• Metagenomic Analysis and Megablast
  Hi, I am using the windshield splatter workflow to analyse my amplicons, However Galaxy Megablas...
• Help with an simple workflow (annotation)?
  Dear all, I need a recommendation about what tools to use in a workflow for annotation of sequenc...
• Can Anyone tell me how to set mismatch number in ncbi blast of Galaxy ?
  I am trying to blast some plant transcripts but the mismatch always results in 1 or 0 in Galaxy ...
• Nucleotide Analysis - Gc Percentage
  Hi all, Are there any built in Galaxy tools that I have missed to do with GC percentage (or inde...