shadow_tr

Services
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Services:

  • Genome Alignment (cellular and viral)
  • De novo assembly
  • Differential gene and/or isoform expression analysis (statistics using edgeR or EBSeq)
  • Fusion gene discovery
  • Nucleotide sequence variation identification
  • Microbiome analysis
  • microRNA seed identification (find all microRNA seeds within any genome and provides output for visualization on genome browser and data on seed localization on all gene features)
  • Circular RNA identification
  • Data transfer (uploading data to sequence databases/archives)
  • Access to Tulane Sphinx Computing Cluster
  • Access to University of Florida High Performance Computing Center
  • Coming soon - Tulane University High Performance Computing Center
  • Seminar Series - "Next Generation Sequence Analysis Learning Series

Methods:

  • Aligners
    • Novoalign
    • Tophat/Bowtie
    • STAR
    • BWA
    • Mrfast
  • De novo assembers
    • Abyss
    • Velvet
    • SOAP (pending)
  • Fusion gene identification
    • FusionSEQ
    • TopHat-Fusion
  • Read visualization
    • Integrated Genome Viewer
  • Blast (Local, batch)
    • Non-restricted nucleotide database
  • Gene and isoform level RPKM analysis
    • SAMMate
    • Cufflinks
    • CummeRbund
    • RSEM
    • eXpress
  • MicroRNA Analysis
    • MiRNAkey
  • Variant Discovery and Analysis
    • VarScan
    • GATK
    • Snape-pooled
    • ANNOVAR
    • CNVnator
    • Variation Hunter
    • SnoopCGH
  • Clinical sequence handling
    • DCBI decrypt (for decrypting patient sequence data from NCBI)
    • Fastq dump (for converting NCBI "sra" formatted sequencing data into "fastq" format for sequence analysis)
    • Aspera for available bandwidth conscious ultra fast transfer of large volumes of data over the internet.
    • Local Galaxy (PSU) server for secure file processing
  • Next Generation Sequence Analysis Learning Series
    • Monthly seminars to provide information to the Tulane community about the capabilities of the Core and instruction on data analysis
      • April 9, 2014 – 1st Floor of the Louisiana Cancer Research Center, “An Introduction to the Tulane Cancer Center Cancer Crusaders NGS Analysis Core and NGS Data Analysis,” Melody Baddoo, MS
      • May 2014 - “Applying programs in Unix for alignment and manipulation of aligned reads”
      • June 2014 – “NGS Data Processing Pipelines and Workflows"

     

1430 Tulane Ave, New Orleans, LA 70112 504-988-5263 medsch@tulane.edu