#acl CscGroup:read

'''RNA-seq Data Analysis'''

= High-Throughput Gene Expression Assays =
 * Next-generation sequencing (NGS)
 * Platforms:
   * Illumina/Solexa's Genome Analyzer, HiSeq systems, MiSeq etc.
   * Applied Biosystems' SOLiD
   * Roche's 454 Life Sciences
   * Helicos BioSciences' HeliScope
 * Terminology
   * Sequencing Depth or Coverage: Total number of reads mapped to the genome/transcriptome, also known as library size.
   * Transcript/gene length: Number of bases in a gene.
   * Read counts: Number of reads mapping to that gene/transcript (expression measurement).
 * Illumina's sequencing technology
   * One flow cell: 8 lanes
   * One lane is often used for the control sample.
   * Multiplexing:
     * a way to save money by sequencing multiple samples on a single unit (an Illumina's flow cell)
     * offers the exibility to construct balanced blocked designs for the purpose of testing differential expression.
   * Barcoding: 
     * to separate inputs, can have many barcodes in a single unit
     * 12 different samples can be indexed with unique subsequences and loaded onto each lane. In total, 96 samples can be sequenced per run.
     * the output can be deconvoluted to individual samples.
 * RNA Sequencing Pipeline