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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Presentation Transcript
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
slide12
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
slide22

Comparative analysis for

denovotranscriptome analysis?

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