Syrah, a Slide-seqV2 pipeline augmentation

Abstract

Spatial transcriptomic techniques such as Slide-seqV2 uncover novel relationships and interactions between cell types by coupling gene expression and spatial data. Here we discuss two unexpected sources of error in Slide-seqV2 data, one physical and one computational. To address this we present an analysis pipeline augmentation, Syrah, which corrects for these errors and show that it improves both data quantity and quality over the standard pipeline alone or in combination with additional sequencing.

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“…Code was retrieved from the Macosko Lab github page: https://github.com/MacoskoLab/slideseq-tools. Reads were mapped to the Sánchez Alvarado lab transcriptome and both mapped read 2 data and unmapped read 1 data were processed using Syrah, a Slide-seqV2 pipeline augmentation, in order to improve read count and reduce noise, resulting in a single digital gene expression matrix for each puck 44,45 .…”