 Hello and welcome to this tutorial on pre-processing 10x single cell RNA-seq data. I am your host, Wendy Bacon from the European Molecular Biology Lab in the European Bioinformatics Institute, or the EMBL EBI, rolls right off the tongue. So we're going to go to transcriptomics, single cell RNA-seq, and then pre-processing of 10x datasets. Okay, and then we're going to start with uploading our data. Copy that, upload data, and we want even more data. Click it again, and here we go. I'm going to be honest, that step can sometimes take quite a long time, so you're very welcome to just import the history that I've already shared. Okay, next up we're going to run RNA star solo. There we go. Okay, so yes, that has our GTF, length 110x, and then we want to select both read 1s, both read 2s. We'll want the whitelist, cell ranger, chemistry version 3, cell ranger 3, and I'm also going to change this to pre-processing 10x datasets. All right, that took a not insignificant amount of time, so now we're going to do, so you can investigate these to your heart's delight. I'm going to go into the multi-QC, that's right, sometimes it doesn't show up when you search for it, so if I go to FSQC quality control, then I can click it, just sometimes things don't search that well. Okay, so we want star, star output log, we want the log, and then you can look at the web page and check out all sorts of worldly things, and now we're going to look at just the star solo output, the log, and lots of things from that. We go down to exponential parameters. All right, and then we can move on to producing a quality count matrix, so we want bundled, and we want barcodes, genes, oh sorry, count, genes, barcodes. All right, and so then we get our lovely new count matrix, which has a mere 272 cells, and then we can go back and we can look at this statistic summary, and we can look at the total number of cells there, and see this 6100. Now we're going to do rank these barcodes, so if I go to droplet QTELS again, okay, format same, same, same, same, the number of rank barcodes, we'll see what happens there, and then we can inspect our lovely new plot and learn lots about this, look at inflection points, etc. Okay, and then now we're going to do filtering, so drop to these cells again, bundled again, and this time we're going to filter for barcodes, but we're going to use what we learned from that plot, empty drops, lower bound we're going to go to 200, tabular, and that brings us to the end of this tutorial, so I hope you have fun.