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• How do I add my own reference genome for mapping RNA-seq data
  How Do I Add my own reference genome for mapping RNAseq data? Below is the link for the referenc...
• Genome Of Interest Is Not Listed
  Dear Sir/Maam I am using Galaxy for analysis of NGS data. I want to map the NGS data, but the ge...
• Preparing for Blast2GO
  Here is my problem: I have used Cuffdiff to determine differential gene expression and extracted...
• Listing genome reference
  Hi, I would like to map reads against genome reference but my genome of interest is not listed. I...
• genome of interest is not listed
  Dear Galaxy team and Galaxy community, I reply on the notice found in HISAT: "If your genome of ...
• 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...
• Extract depth coverage of a particular region from BAM file
  Hi, If any kind soul could help, I loaded BAM files in IGV and i notice some interesting splicin...
• How to add my reference genome to use RNA STAR in usegalaxy.org
  "If your genome of interest is not listed, contact the Galaxy team (--genomeDir)" It is my first ...
• Need help with "Create a BedGraph of genome coverage" tool
  Hi there I am trying to calculate the coverage of my alignment based on the BAM file using "Crea...
• Give a list of genes and return Transcription starting sites as a bed file
  Dear there: I have a questions that may seems naive to most of you: does anyone know if there is...
• How to compare two libraries
  Dear Service, I load in Galaxy server about 10 histories. Each one is composed of a fastq file a...
• pipeline for DNA-seq analysis
  Thanks for all your help. Finally I got the data uploaded on the Galaxy. As suggested there was a...
• Help About Using Sixpack And Get Orf (Genomic Assignment)
  Dear all, So sorry to bother you if you are not interested! I'm doing my genomic assignment...
• Fasta Generation From Pileup For Snp Detection
  I'm interested in generating a fasta file from Ilumina paired reads of my wild type strain. I hav...
• Removing sequence duplicates
  I have used top hat in galaxy to map my files. After mapping i am interested in removing sequence...
• wig to bigwig format in galaxy, unavailable genome
  Hi, I would like to convert a .wig file to a .bigwig file. Should be straightforward, but I am...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Can a genome that's been released be added so I can map against it
  Hi there, I will be mapping my RNAseq reads to a genome of interests soon. Mapping with Bowtie2 ...
• Installing Galaxy
  Dear Galaxy, If I download galaxy on the server of my Institute , will I b...
• Extract Data And New Genes
  Hi Everyone, I am working with *Aedes aegypti * and I obtained around 500 million reads (HiSe...
• Flaking Regions Across Tss
  I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites...
• HISAT2 - no reference genome available
  HISAT2 does not have any options for a built-in reference genome. I need mm10. Source for the r...