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High-Throughput Analysis of Genomic Data [S7] E NRIQUE B LANCO

High-Throughput Analysis of Genomic Data [S7] E NRIQUE B LANCO. NUMBER OF SLIDES: 5 EXPECTED TIME: 15 minutes. RNAseq BIOINFORMATICS ANALYSIS. Quality Control. Expression Quantification. Mapping (splice junctions). Visualization. MAPPING OF SPLICE JUNCTIONS. read. mRNA. PROGRAMS:

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High-Throughput Analysis of Genomic Data [S7] E NRIQUE B LANCO

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  1. High-Throughput Analysis of Genomic Data [S7]ENRIQUE BLANCO NUMBER OF SLIDES: 5 EXPECTED TIME: 15 minutes

  2. RNAseq BIOINFORMATICS ANALYSIS Quality Control Expression Quantification Mapping (splice junctions) Visualization High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013 eblanco@ub.edu

  3. MAPPING OF SPLICE JUNCTIONS read mRNA • PROGRAMS: • TOPHAT • GEM • FORMATS: • SAM EXON (i) DNA read mRNA DNA EXON (i) EXON (i+1) High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013 eblanco@ub.edu

  4. GENE EXPRESSION: RPKMs RPKM: (Reads Per Kilobase of the transcript per Million mapped reads) RPKM is a method of quantifying gene expression from RNA sequencing data by normalizing for total read length and the number of sequencing reads. 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. Vs High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013 eblanco@ub.edu

  5. TRANSCRIPT EXPRESSION: RPKMs Adar 20.489 RPKMs Adar-RA 15 RPKMs Adar-RB 5 RPKMs … http://flux.sammeth.net/capacitor.html • PROGRAMS: • CUFFLINKS • FLUX CAPACITOR High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013 eblanco@ub.edu

  6. VISUALIZATION • PROGRAMS: • UCSC • GBROWSE • FORMATS: • WIG • BEDGRAPH High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013 eblanco@ub.edu

  7. High-Throughput Analysis of Genomic Data [S7]ENRIQUE BLANCO NUMBER OF SLIDES: 5 EXPECTED TIME: 15 minutes

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