High-Throughput Analysis of Genomic Data [S7] ENRIQUE BLANCO

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

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

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

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

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

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

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