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Update 04_cellranger_QC.md
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mistrm82 authored Jul 26, 2024
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Expand Up @@ -121,7 +121,12 @@ Once cellranger has finished running, there will be a folder titled `outs/` in a

The Web Summary HTML file is a great resource for looking at the basic quality of your sample before starting on an analysis. 10x has a [page describing each metric](https://www.10xgenomics.com/analysis-guides/quality-assessment-using-the-cell-ranger-web-summary) in depth. There are two pages/tabs included in a scRNA report titled "Summary" and "Gene Expression".

We have included these Web Summary files for the control and stimulated dataset in the [data](https://www.dropbox.com/s/vop78wq76h02a2f/single_cell_rnaseq.zip?dl=1) provided for the workshop. Please note that some of the values in these reports will be slightly different from current standards, as these samples were generated using the version 1 chemistry kit and optimization have been made since then.
We have included these Web Summary files for the control and stimulated samples as links below. You can **download each, and move the HTML to your project folder**:

* [Control sample](https://www.dropbox.com/scl/fi/skjyyvs9078pbef7s4qvb/ctrl_web_summary.html?rlkey=335gw4qmy29uny5813wg0zakr&dl=1) report
* [Stimulated sample](https://www.dropbox.com/scl/fi/r6n83y57cd7vhc130zm1g/stim_web_summary.html?rlkey=50ur193yfsy5ex9urkmr87h3c&dl=1) report

> **NOTE:** Some of the values in these reports will be slightly different from current standards, as these samples were generated using the version 1 chemistry kit and optimization have been made since then.
### Summary

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## Metrics evaluation

Many of the core pieces of information from the web summary are stored in the `metrics_summary.csv` file. As this is a csv file, we can read it into R and generate plots to include in reports on the general quality of the samples.
Many of the core pieces of information from the web summary are stored in the `metrics_summary.csv`. As this is a csv file, we can read it into R and generate plots to include in reports on the general quality of the samples.

We have included these csv files for the control and stimulated samples as links below. You can right-click on the link and "Save as..." into your project folder:

* [Control sample](https://www.dropbox.com/scl/fi/qnz44ng51ojmhu44acc8g/ctrl_metrics_summary.csv?rlkey=gyk570whhtk3c4z1t4414yne2&dl=1) `metrics.csv` file
* [Stimulated sample](https://www.dropbox.com/scl/fi/gaa4sabcbhwqpuogfh0us/stim_metrics_summary.csv?rlkey=h2uokc9r2edeinxtzgrpw3ds4&dl=1) `metrics.csv` file

First, to read the files in:

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