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

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

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): Vs
High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013

5. TRANSCRIPT EXPRESSION: RPKMs
Adar RPKMs
Adar-RA RPKMs
Adar-RB RPKMs …
PROGRAMS:
CUFFLINKS
FLUX CAPACITOR
High-Throughput Analysis of Genomic Data [S7] - ENRIQUE BLANCO 2013

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

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