Code and Data for "Multiple re-reads of single proteins at single-amino-acid resolution using nanopores"

The primary structures containing data and analysis products are peptidereads_fig2.mat (for figure 2) and peptiderereads_fig3.mat (for figure 3). The main analysis scripts for these data structures are callvariants_fig2.m and reread_analysis_fig3.m respectively. Data for figures S6 (S6_reread_data.dat) and S8 (S8_hetero_data.dat), and the analysis script used to produce figure S6 (S6_reread_analysis.m) are also included. Other files are dependencies of these main scripts. The fields in peptidereads_fig2 are as follows: <strong>folder, eventnum, reducedStart, reducedEnd, suspicious, hasreread:</strong> notes for internal use <strong>variant:</strong> the true identity of the single-amino-acid substitution variant <strong>data: </strong>the ion current data for each read downsampled to 5 kHz. <strong>omit: </strong>whether the read was omitted from analysis due to length <strong>relativeDNAend</strong>: the index in the data where the DNA portion of the read ends. <strong>relativeLinkerEnd:</strong> the index in the data where the linker portion of the read ends. <strong>DNAlevels, Peplevels, Alllevels:</strong> extracted ion current levels for the DNA region, the peptide region, and everything. <strong>cal: </strong>the multiplicative and additive constants applied to calibrate the read <strong>caldata: </strong>the data with calibration constants applied <strong>cons0D, cons0W, cons0G, cons0DNA: </strong>initial guesses for consensuses based on hand curation of data. <strong>pepDcons0, pepWcons0, pepGcons0:</strong> the portion of the handmade consensus with the variant levels. <strong>pepDcons, pepWcons, pepGcons:</strong> the portion of the iterated consensus with the variant levels. <strong>inhandconsensus: </strong>whether the read was used in generation of the inital guess consensuses. <strong>inconsensus</strong>: whether the read was used in generation of either the initial guess or iterated consensuses. <strong>confidence:</strong> the relative likelihood of each variant assigned to the read <strong>incalls:</strong> whether the data was used in variant calling (i.e., not used in consensus generation) <strong>params</strong>: the analysis parameters used