modules/mapdamage2

Log file with a summary of command lines used and timestamps.

A pdf file that displays both fragmentation and misincorporation patterns.

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.

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

Contains a table with read length distributions per strand.

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

A MCMC histogram for the damage parameters and log likelihood.

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

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

Summary statistics for the damage parameters estimated posterior distributions.

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

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

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

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

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

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

Alignments in a FASTA file, only if flagged by -d.

Folder created when —plot-only, —rescale and —stats-only flags are passed.

File containing software versions