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云之南

风声,雨声,读书声,声声入耳;家事,国事,天下事,事事关心

 
 
 

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关于我

专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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http://illumina.ucr.edu/ht/documentation/analysis Data Analysis  

2010-01-04 19:59:10|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://illumina.ucr.edu/ht/documentation/analysis

Data Analysis

Sections

IIGB Bioinformatics Facility provides a wide variety of data analysis services. The following list provides only a general overview. To evaluate all data analysis options for the specific needs of a deep sequencing project, we strongly recommend to discuss them in a meeting with the bioinformatics core director, Thomas Girke.

 

Provided Data Formats

  • Click here for a description of the standard file formats provided for each sequencing run. 

 Quality Reports from Illumina Pipeline Software [PDF Manual]

  • QC of sequencing run

  • Quality filtering and adaptor trimming

  • Basic mapping to reference genome

 

Available Upon Request

  • Online genome browser support

  • Web BLAST server support

 

Custom Data Analyses

  • Comprehensive custom analysis: annotations, mapping, predictions etc.

  • Detailed data analysis reports

  • Statistical analysis

 Please visit the Rates page for pricing information on these services. 

 

UCR Manual on HT-Seq Data Analysis

  • ChIP-seq Analysis

    •  

      general_help.html

    • Example genome browser showing S. cerevisiae (Yeast) chromosomes I and II: Click Here
    • NCBI's Sequence Viewer
      • Illumina Pipeline

        Data Processing Tools

        Alignment Tools [ a more complete link page ]

         

        SNP Calling

         

        De Novo Assembly of Short Reads

         

        Comparative Assembly of Short Readshttp://amos.sourceforge.net/

      • More on this see: "Steven Salzberg assembling genomes from next-generation sequencers"

        •  

          Digital Gene Expression (DGE)

           

          RNA-Seq

           

          Splice Junction Identification

           R & Bioconductor

           

          http://seqanswers.com

        • Google Solexa Group: http://groups.google.com/group/solexa?lnk=srg
        • Genographia next-generation genomics community: No longer online

            Oxford Journals Next Generation Sequencing Article List: "A living resource that we will continually update to include the very latest papers in this area."

          • Bentley, D R, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456: 53-59. http://www.hubmed.org/display.cgi?uids=18987734
          • Dolan, P C, Denver, D R (2008) TileQC: a system for tile-based quality control of Solexa data. BMC Bioinformatics, 9: 250-250. http://www.hubmed.org/display.cgi?uids=18507856
          • Erlich, Y, Mitra, P P, delaBastide, M, McCombie, W R, Hannon, G J (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods, 5: 679-682. http://www.hubmed.org/display.cgi?uids=18604217
          • Rougemont, J, Amzallag, A, Iseli, C, Farinelli, L, Xenarios, I, Naef, F (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics, 9: 431-431. http://www.hubmed.org/display.cgi?uids=18851737
          • 't Hoen, P A, Ariyurek, Y, Thygesen, H H, Vreugdenhil, E, Vossen, R H, de Menezes, R X, Boer, J M, van Ommen, G J, den Dunnen, J T (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res, : . http://www.hubmed.org/display.cgi?uids=18927111
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