One cell per oil droplet โ
and then, what file comes out?
Chromium splits your cells into 100,000 oil droplets and gives each droplet its own 16-letter label. The library built that way goes through a sequencer and comes back as one table.
These 20 lessons look inside that machine first, then take matrix.mtx, features.tsv and web_summary.html apart line by line. At the end you carry one public 10x PBMC sample from the instrument all the way to cell types. Python runs right inside this page. There is nothing to install.
How you'll learn
What goes into the three rows of wells, what happens inside a droplet for 45 minutes โ you see what the hands do first. The files come after.
You learn what the single line 32709 2 4 means. You unpack Matrix Market by hand into a table, and fold and unfold the three CSC arrays inside an HDF5.
Haemoglobin shows up in T cells, and nudging one threshold doubles your cell count. Before you trust a result you feel how you get fooled with your own hands.
Every lesson has a laboratory widget โ how many cells you load, where the knee threshold sits, the three QC cut-offs, the number of PCs, all turned by you.