Pseudo bulking of scATAC-seq

Question

[Manhezz]

Hello,

I have different cell clusters generated using Signac. i want to cal enhancers and super enhancers within a cluster of interest using ROSE algorithm(python ROSE_main.py -g HG37 -i enhancers.gff -r BAM -o Hezz -s 12500 -t 2500), using this code how do i come up with the bam file for each cluster? data type is scATAC

Answer 1

[jared.andrews07]

Use sinto to split the bam into one for each cluster by feeding in the barcodes of cells for each cluster.