As in our previous work (Crow et al, 2017), Bowtie (v 0.12.7) was used for sequence alignment of read2 (polyA primed) to the mouse reference genome (mm9), while read1 sequences were used for UMI (varietal-tag) counting. A custom python script was used Bowtie (v 0.12.7) was used for sequence alignment of read2 (polyA primed) to the mouse reference genome (mm9), while read1 sequences were used for UMI (varietal-tag) counting. Multiple reads to the same gene with the same tag sequences were rejected and only counted as one, such that only mapped sequences with unique tags were retained and tallied for each mRNA for each cell.
