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 analysis with reference genome

RNA seq analysiswith reference genome


Dataset

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

Import Genome information

  • NC000082subset.gbk


Start rna seq analysis

Start RNA seq analysis


Select reference with annotation

Select Reference with annotation


Setting mapping argument

Setting mapping argument


Setting exon argument

setting Exon argument


Rna seq analysis with reference genome

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

Exercise:

  • Import Liver Reads

  • do above steps


Expression analysis

Expression analysis


Experiment table for comparision

Experiment Table for Comparision


Rna seq analysis with reference genome

  • Comparative analysis for

    denovotranscriptome analysis?


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