Initial rough analysis of variant loss in selection experiments. Roughly 80% of library variants are being filtered out because they have fewer than 20 counts. This notebook analyzes filtered variants from selections with libA and libB against AUSAB-13 on 220606, and tries to address whether variants are being lost due to bottlenecking during rescue / passaging, or functional selection.
Will expand this analysis once we get higher sequencing coverage for these samples, as low sequencing depth is likely exacerbating variant loss.
Initial rough analysis of variant loss in selection experiments. Roughly 80% of library variants are being filtered out because they have fewer than 20 counts. This notebook analyzes filtered variants from selections with libA and libB against AUSAB-13 on 220606, and tries to address whether variants are being lost due to bottlenecking during rescue / passaging, or functional selection.
Will expand this analysis once we get higher sequencing coverage for these samples, as low sequencing depth is likely exacerbating variant loss.