Issues & possible solutions

Reproducing Greenleaf paper code

Old and outdated code Some data could not be found in original scripts

optimizeLSI (LSI for atac in archR but not for RNA)

Updated to work

Package versions python 2.7 & seurat 3.x

macs2 issue

path to macs2

Need celltypes for integration

FeatureMatrix issue

time consuming (works with 32 cores 32gb each)