Smart-Seq was developed as a single-cell sequencing protocol with improved read coverage across transcripts.

The pipeline can automatically analyze Smart-Seq sequencing data and produces a series of visual figures and tables of results. In this pipeline, both human and mouse species are supported. The pipeline consists of five analysis steps. Firstly, trimmomatic software was used for quality control. For reads after quality control, STAR software is used for mapping. Then, a gene expression matrix can be obtained by using featureCounts software.

The schematic diagram of Smart-Seq pipeline is as follows:

Software and references:

Trimmomatic:Trimmomatic: a flexible trimmer for Illumina sequence data.
STAR:Mapping Smart-Seq Reads with STAR.
featureCounts:featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
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