Tutorial: demultiplexing prefrontal cortex scATAC-seq data

We prepared prefrontal cortex scATAC-seq (PRJNA729525) synthetic mixture data for users who are new to scAVENGERS. To note, the clustering performance is inevitably low because we subsampled part of chromosome 1 to reduce the size of the data, so that most of the call barcodes will be unassigned.

Downloading the data

The data will be prepared after running the script below. The directory examples is where the data are in. Note that the genome fasta file must be decompressed. If the genome fasta file is not decompressed, the whole pipeline will halt when running vartrix.

wget https://github.com/kaistcbfg/scAVENGERS/releases/download/v0.1.0/examples.tar.gz
tar -xvzf examples.tar.gz
cd examples
gzip -d genome.fa.gz

Executing scAVENGERS

After setting your current directory into scAVENGERS_example, running scAVENGERS pipeline will produce results under the directory named outdir.

scAVENGERS pipeline -j 10 --configfile config.yaml