Morris A. Swertz University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands

The sequencer is producing reads (in FastQ format) and are aligned to the hg19 reference genome with STAR (Dobin A et al. ¹). Dropseq (Macosko EZ et al [3]) was used for flaging individual cells and UMI's. The gene level quantification was performed again by using Dropseq filtering readcount on unique UMI's. Picard tools (Picard Sourceforge ²) is used for sorting, merging or format converting SAM/BAM files.

1. Dobin A, Davis CA, Gingeras TR: STAR: ultrafast universal RNA-seq aligner. 10.1093 bts635 Bioinformatics (2012)
2. Picard Sourceforge Web site. http://picard.sourceforge.net/ ${picardVersion}
3. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Macosko EZ et al,Cell, 2015