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We have implemented QuickRNASeq, an open-source based pipeline for large scale RNA-seq data analysis. QuickRNASeq takes advantage of parallel computing resources, a careful selection of previously published algorithms for RNA-seq read mapping, counting and quality control, and a three-stage strategy to build a fully automated workflow. We also implemented built-in functionalities to detect sample swapping or mislabeling in large-scale RNA-seq studies.
Our pipeline significantly lifts large-scale RNA-seq data analysis to the next level of automation and visualization. Please take a look at our test run project report and get a taste of its rich interactive visualization features. http://baohongz.github.io/QuickRNASeq
QuickRNASeq user guide can be downloaded or is accessible online as well
http://baohongz.github.io/QuickRNASeq/guide.html
For more on QuickRNASeq, please see our paper http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2356-9
Enjoy QuickRNASeq
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