# 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.pdf`

A 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.pdf`

Contains a table with occurrences for each type of mutations and relative positions from the reads ends.

`misincorporation.txt`

Contains frequencies of Cytosine to Thymine mutations per position from the 5’-ends.

`5pCtoT_freq.txt`

Contains frequencies of Guanine to Adenine mutations per position from the 3’-ends.

`3pGtoA_freq.txt`

Contains a table of the reference genome base composition per position, inside reads and adjacent regions.

`dnacomp.txt`

Contains a table with read length distributions per strand.

`lgdistribution.txt`

A MCMC histogram for the damage parameters and log likelihood.

`Stats_out_MCMC_hist.pdf`

Values for the damage parameters and log likelihood in each MCMC iteration.

`Stats_out_MCMC_iter.csv`

A MCMC trace plot for the damage parameters and log likelihood.

`Stats_out_MCMC_trace.pdf`

Summary statistics for the damage parameters estimated posterior distributions.

`Stats_out_MCMC_iter_summ_stat.csv`

Empirical misincorporation frequency and posterior predictive intervals from the fitted model.

`Stats_out_MCMC_post_pred.pdf`

Position specific probability of a C->T and G->A misincorporation is due to damage.

`Stats_out_MCMC_correct_prob.csv`

Contains the global reference genome base composition (computed by seqtk).

`dnacomp_genome.csv`

Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores.

`*.{bam}`