PMSB Project: RNA- Seq Read Simulation

PMSB Project: RNA-Seq Read Simulation

Overview • The actualprocessofRNA-Seqisquiteinvolved • For simple simulation, wecan break it down totwosteps: • Simulatesplicingof genes in theorganism • Simulatesamplingprocessbythesequencingmachine. Titel, Datum

Part A: Simulate Splicing • Read in: • Reference Sequence • Gene/Exon/Intro annotation from GFF (GTF File) • Generate transcriptome of organism • For each gene • For each mRNA • Splice together sequences from genome • Write out transcriptome to FASTA File Titel, Datum

Part B: Read Simulation • Read in • Reference sequence (transcriptome) • Read in expression levels (aka counts) for each transcript • Simulate Reads • Single-End: Sample uniformly with fixed length. • Paired-End: Sample paired, insert size follows normal distribution. • Error Model: Uniform Errors • Error Model: Read in FASTQ files, convert quality values into error probabilities, use this form position dependent errors. • Write out simulated reads Titel, Datum

PMSB Project: RNA- Seq Read Simulation

PMSB Project: RNA- Seq Read Simulation

Presentation Transcript

RNA-Seq

RNA- seq library prep introduction

RNA-Seq and transcriptome analysis

RNA- seq Analysis

RNA- Seq Lab

Measuring transcriptomes with RNA-Seq

RNA seq (I)

Biases in RNA- Seq data

Le RNA-seq

Bioinformatics for DNA - seq and RNA- seq experiments

RNA- seq Analysis Practical Exercise

Statistics for RNA- seq Analysis

RNA-Seq and transcriptome analysis

RNA-seq data

RNA-Seq datasets

RNA- seq Analysis in Galaxy

RNA-SEQ