modules/mapdamage2
Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
Description
Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
Output
A pdf file that displays both fragmentation and misincorporation patterns.
Fragmisincorporation_plot.pdfA pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand.
Length_plot.pdfContains a table with occurrences for each type of mutations and relative positions from the reads ends.
misincorporation.txtContains frequencies of Cytosine to Thymine mutations per position from the 5'-ends.
5pCtoT_freq.txtContains frequencies of Guanine to Adenine mutations per position from the 3'-ends.
3pGtoA_freq.txtContains a table of the reference genome base composition per position, inside reads and adjacent regions.
dnacomp.txtA MCMC histogram for the damage parameters and log likelihood.
Stats_out_MCMC_hist.pdfValues for the damage parameters and log likelihood in each MCMC iteration.
Stats_out_MCMC_iter.csvA MCMC trace plot for the damage parameters and log likelihood.
Stats_out_MCMC_trace.pdfSummary statistics for the damage parameters estimated posterior distributions.
Stats_out_MCMC_iter_summ_stat.csvEmpirical misincorporation frequency and posterior predictive intervals from the fitted model.
Stats_out_MCMC_post_pred.pdfPosition specific probability of a C->T and G->A misincorporation is due to damage.
Stats_out_MCMC_correct_prob.csvContains the global reference genome base composition (computed by seqtk).
dnacomp_genome.csvRescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.
*.{bam}