Table 1.

Overview of notations

Notation	Definition
$X_{n,j}^W$	The number of Strand-seq reads from single cell j mapped to the n-th PacBio read in Watson direction
$X_{n,j}^C$	The number of Strand-seq reads from single cell j mapped to the n-th PacBio read in Crick direction
$X_{n,j}$	$(X_{n,j}^W,X_{n,j}^C)$
$X_n^C$	$(X_{n,1}^C,\dots ,X_{n,J}^C)$
$X_n^W$	$(X_{n,1}^W,\dots ,X_{n,J}^W)$
$X_n$	$(X_{n,1},\dots ,X_{n,J})$
T	The set of all possible strand states {WW, WC, CC}
$t_{k,j}\in T$	The state of single cell j in cluster k
$t_k$	$(t_{k,1},\dots ,t_{k,J})$
${\theta }_{k,j,t}$	The probability that single cell j has state t in cluster k
${\theta }_{k,j}$	$({\theta }_{k,j,\text{WW}},{\theta }_{k,j,\text{WC}},{\theta }_{k,j,\text{CC}})$
${\theta }_k$	$({\theta }_{k1},\dots ,{\theta }_{kJ})$
πk	The probability that a PacBio read comes from cluster k
$Z_{n,k}$	A binary random variable showing whether PacBio read n comes from cluster k
$[1:a]$	The set of all integers between 1 and a