RNA-seq stranded coverage and junctions generated by STAR 2.6.1b

Coverages were normalized using RNA-seq log-ratio normalization factors.
Afterward, coverages were combined to the mean coverage for each experiment group.

Notes on the STAR index used for alignment:

• Wildtype samples were aligned versus the mouse mm39 genome, using Gencode vM33 comprehensive gene annotations.
• Mutant samples were aligned versus the mm39 modified in two ways:
1. A custom chromosome chrAdam19TdT was added which contained the full mutant Adam19 construct Adam19_TdTomato obtained by Sanger sequencing.
2. The wildtype Adam19 region region on chr11 masked to prevent competitive alignment of mutant samples with the wildtype and mutant sequences for Adam19.

These changes were made to prevent spurious, competitive alignment of wildtype RNA-seq reads to parts of the mutant Adam19_TdTomato construct; similarly to prevent mutant RNA-seq reads from competitive alignment to parts of the wildtype Adam19 region on chr11.