Basic Clustering Walk-through
Contents
Basic Clustering Walk-through¶
Section table of contents¶
Input Files¶
For 100Kb bins clustering¶
The dataset we used for 100Kb clustering documentation comes from the hippocampus (HIP) of adult P56 male mice. These datasets belong to a larger mouse brain methylome atlas dataset [Liu et al., 2021].
Download Input Files¶
Cell metadata: ADD DOWNLOAD URL
single-cell ALLC files: ADD DOWNLOAD URL
MCDS files: ADD DOWNLOAD URL
Prepare your own datasets¶
Cell metadata¶
Using the sample dataset above as an example. The cell metadata file is a user-defined file that has no fixed format. It usually contains mapping metric and experimental design metadata for each cell. We use this file to perform some basic filtering to remove low quality cells.
Single-cell ALLC files¶
See allcools bam-to-allc for how to generate single-cell ALLC files
from filtered single-cell BAM files.
MCDS files¶
See allcools generate-dataset for how to generate MCDS files containing raw count matrix, and/or hypo-/hyper-methylation score matrix for any kinds of genomic features.