In ShawHahnLab/microsat: Computational, High-throughput Individual Identification through Microsatellite Profiling

Flagged Values

fig_height_flag <- 2 + num_samples * num_replicates / 6

Possible PCR Stutter Removed

These tables show samples that had a candidate allele filtered out because it was potential PCR stutter.

plot_heatmap_stutter(results)

Possible PCR Artifacts Removed

These tables show samples that had a candidate allele filtered out because it was a potential (non-stutter) PCR artifact.

plot_heatmap_artifacts(results)

More than Two Prominent Sequences

These tables are color-coded to show samples with more than two abundant sequences still present after all filtering. Cases with more than two could imply contamination or excessive PCR stutter or artifacts obscuring the correct allele sequences.

plot_heatmap_prominent_seqs(results)

Proportion of Allele-Matching Reads

These tables are color-coded by the proportion of locus-matching reads represented by the called alleles per sample, running from red for 0% to white for 100%. The proportion is calculated for both alleles and color-coded with the same color for both.

plot_heatmap_proportions(results)

Possible Homozygous Samples

These tables show which samples are reported as homozygous.

plot_heatmap_homozygous(results)

ShawHahnLab/microsat documentation built on Aug. 25, 2023, 11:16 p.m.