Getting started with spatial data
Check with the core to get the following information Files: These are specific to each run CSV files related to the run which has well number, slide serial number and and other information Figure out the method, sequencing chemistry and other specifics of the run Index barcodes if you are running bcl2fastq Fastq files if you are not running bcl2fastq Download the following files from 10X website Run space ranger mkfastq or bcl2fastq to get the fastq files If you already have fastq, skip this step Using Loupe browser, depending on the type of assay (ex: Visium vs Visium HD), align cytassist and the polaris images You also need to know their well ID which can be found from the csv files you get from spatial core You might have to edit the json file to include the right slide serial number and well for visium. For visium HD, this is not needed Run it on each area separately Input requirements: fastq files, reference file, probe id file, alignment json for each sample, cytassist and polaris scans for each sample.
Files from spatial core
Alignments/Image registration from loupe GUI
Slide serial number here is visium slide ID
