Commit 9d437a5e authored by Davis McCarthy's avatar Davis McCarthy
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Updating README

parent 6303b48f
......@@ -29,7 +29,7 @@ We have two 1.5 hour sessions to work on single-cell methylation. Broadly, we wi
1. Negative controls should not align
1. bisulfite conversion efficiency (assessed using CHH methylation from bismark reports) should be >95%
1. mapping efficiency (from bismark reports) >10% (30-40% is normal here but may end up lower in these practicals)
1. number of CpG sites covered (I use 1M unique positions but this will depend on seq depth so maybe just exclude outliers)
1. number of CpG sites covered (we often use 1M unique positions but this will depend on sequencing depth so can also exclude outliers)
3. Preprocessing and annotation
* Quantify methylation over regions of interest (promoters, gene bodies, enhancers, repeats, CpG islands).
1. mean methylation rate (each covered position counts once – i.e. do not give extra weight to positions with >1 read)
......@@ -40,7 +40,7 @@ We have two 1.5 hour sessions to work on single-cell methylation. Broadly, we wi
1. Dimension reduction
1. Clustering
We will manage the data processing and analysis "pipeline" using [snakemake](http://snakemake.readthedocs.io/en/stable/). We will analyze our results in RStudio, using an [R Markdown](http://rmarkdown.rstudio.com) Notebook (see the `notebooks` folder in this repository for an example.)
We will manage the data processing and analysis workflow using [Snakemake](http://snakemake.readthedocs.io/en/stable/). We will analyze our results in RStudio, using an [R Markdown](http://rmarkdown.rstudio.com) Notebook (see the `notebooks` folder in this repository for an example.)
## Data
......@@ -73,7 +73,7 @@ in case you wish to use it for the second part of the analysis.
* [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* [`MultiQC`](http://multiqc.info/)
* [`MethylQA`](http://methylqa.sourceforge.net/index.php)
* [`Singularity`][https://www.sylabs.io/docs/]
* [`Singularity`](https://www.sylabs.io/docs/)
## Acknowledgements
......
Supports Markdown
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