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PMSB Project: RNA- Seq Read Simulation

PMSB Project: RNA- Seq Read Simulation. Overview. The actual process of RNA- Seq is quite involved For simple simulation , we can break it down to two steps : Simulate splicing of genes in the organism Simulate sampling process by the sequencing machine . Part A: Simulate Splicing.

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PMSB Project: RNA- Seq Read Simulation

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  1. PMSB Project: RNA-Seq Read Simulation

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

  3. 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

  4. 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

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