Software to support titled: Self-cleaving guide RNAs enable pharmacological selection of precise gene editing events in vivo.

For the custom alignments, Bowtie version 1 was used to create custom indexes and align data from knock in mouse model.  Indexes were made from selected knock in sequence and transcripts of targeted genes.  Default parameters were used to build indexes.  A 50 base wide window (shifted in steps of 15 bases) was used to go through the sequenced data looking for alignments and selected the first valid alignment found.  For valid alignments, 3 mismatches were allowed, but required unique best matches (--best --strata -v  3 –m 1).  Once all alignments were found, full sequences were stacked based on positions of windowed alignment. This allowed us to see the “overhang” (in an unbiased way) where our knock in sequence was inserted into the host genome (mouse genome assembly GRCm38).  Paired end sequencing was performed, but aligned to pair ends independently.  The alignment strategy did not generate many mated pairs and mated pairs were not required, but when counting alignments, mated pairs were only counted once.