![]() The input could be one or more BAM files. RNA-SeQC is implemented in Java and is not required installation, however can be run using the GenePattern web interface. Essentially, provides three types of quality control: read counts (such as duplicate reads, mapped reads and mapped unique reads, rRNA reads, transcript-annotated reads, strand specificity), coverage (like mean coverage, mean coefficient of variation, 5’/3’ coverage, gaps in coverage, GC bias) and expression correlation (the tool provides RPKM-based estimation of expression levels). RNA-SeQC is a tool with application in experiment design, process optimization and quality control before computational analysis.S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. ![]()
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