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update README #45
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sreichl committed Sep 14, 2024
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Expand Up @@ -123,10 +123,11 @@ Below are some guidelines for the manual quality control of each sample, but kee
- Compare all samples to the best, based on above's QC metrics.
- Check cell type / experiment-specific markers or sex chromosome (`X`/`Y`) for accessibility as positive controls.
- Check e.g., developmental regions for accessibility as negative controls.
> [!IMPORTANT]
> Sometimes reads map to `Y` in females, because `X` and `Y` chromosomes both have [pseudoautosomal regions (PARs)](https://www.ensembl.org/info/genome/genebuild/human_PARS.html) that are common between the two chromosomes.
6. [Unsupervised Analysis](https://github.com/epigen/unsupervised_analysis) (e.g., PCA or UMAP)
- Identify outliers/drivers of variation, especially in the control samples and within replicates.

> [!IMPORTANT]
> Sometimes reads map to `Y` in females, because `X` and `Y` chromosomes both have [pseudoautosomal regions (PARs)](https://www.ensembl.org/info/genome/genebuild/human_PARS.html) that are common between the two chromosomes.
My personal QC value scheme to inform downstream analyses (e.g., unsupervised analysis)
- 0 = did not pass
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