Info about the BINF 3121 Statistics for Bioinformatics class:

• user pkulzer@charlotte.edu is added in the "Teacher" role
• to log into the class web site (that uses canvas) visit https://canvas.charlotte.edu
• once you've logged in, you can visit the class web site using this URL: https://instructure.charlotte.edu/courses/244309
• if you lose track of the previous URL, you can also find the class by logging into canvas.charlotte.edu and searching for "202580-BINF-3121-001-11340" (BINF 3121) fall 2025
• to see the Seurat tutorial key, visit the Grades page in the course web site and view the submission by "Test Student"
• note that the tutorial has some code that produces a data file reporting cluster assignments for each cell that made it through the quality-control and clustering steps. We can easily write new code (using the existing code as inspiration!) to create whatever files and formats might be needed to get IGB to color-code alignments by cluster identity.
• The previous assignment has a link to a video that everybody was supposed to watch. The video is a public lecture by Aviv Regev, a researcher who co-developed single cell RNA-Seq. I highly recommend watching the video before creating the tutorial!

Update:

The "10K pbmc" dataset (human) we discussed last week is indeed available in the input format we need for Seurat.

The Web page describing the dataset is here:

• https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-v3-1-chromium-x-without-introns-3-1-high

One thing that seems a little weird is the naming for this dataset:

*10k Human PBMCs, 3' v3.1, Chromium X (without intronic reads)

What does "without intronic reads" mean? Is there another release of these same data where intronic reads were included?

Here's how to get the associated data files required for next steps analyses:

• download https://cf.10xgenomics.com/samples/cell-exp/6.1.2/10k_PBMC_3p_nextgem_Chromium_X/10k_PBMC_3p_nextgem_Chromium_X_filtered_feature_bc_matrix.tar.gz
• unpack and untar the file

Here are the commands I used to do this on my Mac, after installing handy internet downloader command "wget"

wget https://cf.10xgenomics.com/samples/cell-exp/6.1.2/10k_PBMC_3p_nextgem_Chromium_X/10k_PBMC_3p_nextgem_Chromium_X_filtered_feature_bc_matrix.tar.gz
gunzip 10k_PBMC_3p_nextgem_Chromium_X_filtered_feature_bc_matrix.tar.gz
tar -xf 10k_PBMC_3p_nextgem_Chromium_X_filtered_feature_bc_matrix.tar

The final "tar" command creates a new directory on your machine named "filtered_feature_bc_matrix" with these contents.

• matrix.mtx.gz - compressed data table where columns are cells and rows are genes (features)
• barcodes.tsv.gz - compressed list of all cell barcodes (column headings for the data table)
• features.tsv.gz - compressed list of all genes that were measured in the 10x data processing pipeline

These are the three files Seurat data analysis software requires. No doubt other software expects these same files.

attn: Nowlan Freese, Karthik Raveendran and Paige Kulzer

I will see if I can run the Seurat code over these data to create a UMAP plot.

Ann Loraine - I'm not sure what the "without intronic reads" means. I was hoping it meant less junk data in the introns, but there still seemed to be lots of reads in introns. I just needed a dataset that included the bam and cloupe file. There are two other related files on the 10X website. One that is "with intronic reads" and another file that doesn't distinguish (link).

I've created a rough first draft (sans images) which I'd like to review so that we can finalize the content of the tutorial before adding images and final touches!

This example tutorial is located within the Loraine Lab shared Google Drive folder.

As the class this tutorial was created for has finished, closing ticket.