CURIOSEEKER_GEN_GENE_BARCODE_UMI_DB step failed with the following error. How do I resolve it?

GEN_GENE_BARCODE_UMI_DB, CURIOSEEKER_GEN_GENE_BARCODE_UMI_DB, pyarrow Failure mode. Process name: NF:CURIOSEEKER:PRIMARY_JOINED:CURIOSEEKER_GEN_GENE_BARCODE_UMI_DB pyarrow.lib.ArrowNotImplementedError:Unsupported cast from string to null using function cast_null) Answer This is a sporadic error that will have a permanent fix in V3 of the Curio Seeker Bioinformatics Pipeline. There are two ways to [...]

If I have multiple regions or tissues of interest on a tile, how do I select only the beads for the region I am interested in?

One way to do this is through seurat. It has an interactive plotting function, where you can draw around an area and it will return a list of cells/beads within the boundary you draw. See link below (section interactive plotting features). Please note the vignette describing the two ways to perform interactive plotting. [...]

How do you get untrimmed reads from the sequencer?

Some customers get trimmed reads automatically during demultiplexing (demux) from the sequencing core. Here is how you get the untrimmed reads. During demultiplexing there is an option to remove the common adapter sequence. If you turn this option off, the reads will be constant [...]

What method of clustering do we use for the UMAP?

Bioinformatics details on how we do unbiased clustering. We used Seurat's FindClusters() function with algorithm=1, which uses "Louvain algorithm” for modularity optimization. For UMAP, we use Seurat’s RunUMAP() function on the top 30 principal components. If there are fewer than 30 pc identified, we will use all identified [...]

What is the conversion of coordinate system to um?

1 pixel = [...]