It is proposed to update/refactor the handling of metadata and QC protocols for 10x Genomics Visium projects, as the current set of recognised metadata values is rather haphazard and has led to a proliferation of associated QC protocols which only differ by name.
The starting point is the 10x Genomics overview of its Visium platform:
HD Spatial Gene Expression (compatible with FFPE tissue samples & uses CytAssist for analyte capture)
Spatial Gene Expression (compatible with FFPE, fresh frozen and fixed frozen samples & uses CytAssist; can also use direct placement for FFPE samples)
Spatial Gene + Protein Expression (compatible with FFPE samples only & uses CytAssist)
Also: all of these use a 50bp insert in read 2, except for Spatial Gene Expression (which has a 90bp insert); this information is used in the Visium QC protocols to generate "mapped" metrics from just the relevant part of read 2.
It is proposed to update/refactor the handling of metadata and QC protocols for 10x Genomics Visium projects, as the current set of recognised metadata values is rather haphazard and has led to a proliferation of associated QC protocols which only differ by name.
The starting point is the 10x Genomics overview of its Visium platform:
https://www.10xgenomics.com/platforms/visium
which lists 3 types of "assay":
Also: all of these use a 50bp insert in read 2, except for Spatial Gene Expression (which has a 90bp insert); this information is used in the Visium QC protocols to generate "mapped" metrics from just the relevant part of read 2.