Demultiplexing and preprocessing for custom single-nucleus Drop-seq data
I didn't notice the sentence:


  Paired-end sequencing reads were processed largely as described (http://mccarrolllab.com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf ), with additional correction steps.


This should provide instructions on how to lead the preprocessing and mapping of data.