Great overview of RNA-seq tool pipelines
Not the most recent paper but still a pretty good starting point for deciding what tool you're going to use in your experiment. Also, things like QA and aligning from this paper can be used when working with other sequencing methods.
Computational methods for transcriptome annotation and quantification using RNA-seq : Nature Methods : Nature Publishing Group
High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. …
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