Rna seq analysis with reference genome
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RNA seq analysis with reference genome. Dataset. Reference genome mouse chromosome 16 subset, 13Mbp (complete chr16, 98Mbp) Reads Brain Liver.

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RNA seq analysis with reference genome

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RNA seq analysiswith reference genome


Dataset

  • Reference genome

    • mouse chromosome 16 subset, 13Mbp

      (complete chr16, 98Mbp)

  • Reads

    • Brain

    • Liver

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods, 5(7):621-628.


Import Genome information

  • NC000082subset.gbk


Start RNA seq analysis


Select Reference with annotation


Setting mapping argument


setting Exon argument


RPKM

  • Read per kilobase of exon model per million mapped reads

  • # total mapped reads

  • Mapped contig/exon length

Mortazavi, A. et.al. (2008). Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods,

5(7):621--628.


Exercise:

  • Import Liver Reads

  • do above steps


Expression analysis


Experiment Table for Comparision


  • Comparative analysis for

    denovotranscriptome analysis?


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