In DNA methylation tutorial, the data for matrices construction and secondary processing are not consistant.

[qrzhang]

Hi EpiScanpy team,

Thanks for such a powerful tool 👍

Recently, I'm working on using epiScanpy on single cell DNA methylation data by following your tutorials. I find one notebook for matrices preparation (link) and another for secondary processing (link)

However, see screenshots below, the data you provided for the first tutorial is based on promoters while it is based on enhancers for the second tutorial.

------------------------------------------------ Matrices preparation -------------------------------------------------------

------------------------------------------------ Secondary processing ------------------------------------------------------

So, do you know where I can find the consistent tutorials for single cell DNA methylation data? Or, I will appreciate it if you can share me the bed files you used to get the enhancer mCG anndata in the second notebook (link)

Thanks a lot,

Qian :)

[DaneseAnna]

Hi,
Thank you for your interest.

You can find the bed file containing the enhancer information here: https://www.dropbox.com/s/m4hlo6qeinu4byq/cortex_enhancer.bed?dl=0

We are about to update the website and will release new tutorials very soon, we will make it more consistent. In the mean time, if you want to play with methylation data and its processing you can find the fully built enhancer count matrix here : https://www.dropbox.com/s/v7j6csma973t6k9/enhancer_c1_CG_noimputation.h5ad?dl=0

Don't hesitate to contact us again if you have any other inquiry.

Best,
Anna