USAGE

Install

python setup.py install

preprocessing

• generate a cleaned BAM file from cellranger BAM output: $ samtools view -@ 20 -h -b -f 2 -F 1024 possorted_bam.bam > possorted_uniq_mapped_proper.bam

• run count_mapped_per_cell.sh script to calculate background counts in the scCUT&TAG data.

normalize read counts in both ADT and scCUT&TAG counts