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• Using the Extract Genomic DNA tool in Galaxy
  Hi everyone! So I am trying to use the the NGS: SAMtools function in galaxy to generate consensu...
• Finding Open Reading Frames And Corresponding Genes
  Hi I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using b...
• User Reference Vs. Built-In Index
  Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The work...
• Which reference to map against for RNA-Seq using HISAT2
  Hi all, I am trying to determine differential expression between two test conditions - in rat. T...
• How to use ANNOVAR with bacterial genome?
  I am trying to automatically generate annotations for a VCF file generated from the Mtb H37Rv gen...
• Variant analysis help
  Hello, I am trying to identify variants using data from a BAM file generated from an RNA-Seq exp...
• problem with diamond
  Hello. I am trying to use diamond but fail to do so, due there was no reference genome...
• TopHat Build in genomes
  Hello I'm new in using TopHat for RNAseq data analysis I'm trying to align fastq files that gene...
• unable to load zebrafish GTF/GFF3 files from current history into any of the RNA analysis tools
  I am analyzing zebrafish RNA seq data, I am able to upload the fastq files, use trimmomatic, alig...
• Dockers vs local through VM
  I am very new to bioinformatics and computer knowledge on linux or command based programming is v...
• Problem with the tool: Extract Genomic DNA
  Hi! I'm new with bio-info analysis and I'm doing my first ChIP-Seq analysis with Galaxy. I follow...
• How to create a pseudomolecule?
  Hello I am thankful to the galaxy team for providing a wonderful platform for analyses. I am usi...
• Inbuilt reference genome
  Hi, I ran a top hat analysis on samples, but after the cuffdiff step, I do not have any genes an...
• Workflow with collections
  The task was to download several SRAs from NCBI, align to reference genome, find SNPs. I made man...
• why do Galaxy have a reference genome of sheep?
  Hi: I am analyzing RNA-seq data of sheep using Galaxy. But I can not find a reference genome abou...
• Rna Seq Analysis
  I am new to Galaxy and I am not sure whether these topics were discussed earlier. I followed the ...
• Operate On Genomic Intervals
  Hello, I have binned the mouse genome into fragments based on restriction enzyme cut site...
• Snp Finding
  Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I...
• Tophat in Cloudman: missing built-in genome
  Hell all, After several days of struggling, I finally managed to set up a Galaxy instance in Clo...
• use HIV as reference genome
  hi, i have 4  read outs that cover the whole genome of HIV sequence. i want to align them to for...
• 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...