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RNA seq analysis with reference genome

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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  1. RNA seq analysiswith reference genome

  2. 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.

  3. Import Genome information • NC000082subset.gbk

  4. Start RNA seq analysis

  5. Select Reference with annotation

  6. Setting mapping argument

  7. setting Exon argument

  8. 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.

  9. Exercise: • Import Liver Reads • do above steps

  10. Expression analysis

  11. Experiment Table for Comparision

  12. Comparative analysis for denovotranscriptome analysis?

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