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This RNA-Seq analysis pipeline uses an annotated genome to identify differentially expressed genes and it consists of the following steps:differential expressed genes/transcripts. 6 hour minimum ($282 internal, $360 external) per project.

1. Quality Assessment

Data quality assessed using industry standard tools and quality assessment evaluated prior to downstream analysis.

  •  Deliverables: Reports generated by FastQC.

 Tools Used:

  • FastQC(Andrews 2010) used to generate quality summaries of data:
    • Per base sequence quality report: useful for deciding if trimming necessary.
    • Sequence duplication levels: evaluation of library complexity. Higher levels of sequence duplication may be expected for high coverage RNAseq data.
    • Overrepresented sequences: evaluation of adapter contamination.

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