.TH MAPDAMAGE "1" "August 2016" "mapDamage 2.0.6" "User Commands"
.SH NAME
mapDamage \- tracking and quantifying damage patterns in ancient DNA sequences
.SH SYNOPSIS
.B mapDamage
[\fI\,options\/\fR] \fI\,-i BAMfile -r reference.fasta\/\fR
.SH DESCRIPTION
MapDamage is a computational framework written in Python and R, which
tracks and quantifies DNA damage patterns among ancient DNA sequencing
reads generated by Next-Generation Sequencing platforms.
.SH OPTIONS
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.IP
Input files:
.TP
\fB\-i\fR FILENAME, \fB\-\-input\fR=\fI\,FILENAME\/\fR
SAM/BAM file, must contain a valid header, use '\-' for
reading a BAM from stdin
.TP
\fB\-r\fR REF, \fB\-\-reference\fR=\fI\,REF\/\fR
Reference file in FASTA format
.IP
General options:
.TP
\fB\-n\fR DOWNSAMPLE, \fB\-\-downsample\fR=\fI\,DOWNSAMPLE\/\fR
Downsample to a randomly selected fraction of the
reads (if 0 < DOWNSAMPLE < 1), or a fixed number of
randomly selected reads (if DOWNSAMPLE >= 1). By
default, no downsampling is performed.
.TP
\fB\-\-downsample\-seed\fR=\fI\,DOWNSAMPLE_SEED\/\fR
Seed value to use for downsampling. See documentation
for py module 'random' for default behavior.
.TP
\fB\-\-merge\-reference\-sequences\fR
Ignore referece sequence names when tabulating reads
(using '*' instead). Useful for alignments with a
large number of reference sequnces, which may
otherwise result in excessive memory or disk usage due
to the number of tables generated.
.TP
\fB\-l\fR LENGTH, \fB\-\-length\fR=\fI\,LENGTH\/\fR
read length, in nucleotides to consider [70]
.TP
\fB\-a\fR AROUND, \fB\-\-around\fR=\fI\,AROUND\/\fR
nucleotides to retrieve before/after reads [10]
.TP
\fB\-Q\fR MINQUAL, \fB\-\-min\-basequal\fR=\fI\,MINQUAL\/\fR
minimum base quality Phred score considered, Phred\-33
assumed [0]
.TP
\fB\-d\fR FOLDER, \fB\-\-folder\fR=\fI\,FOLDER\/\fR
folder name to store results [results_FILENAME]
.TP
\fB\-f\fR, \fB\-\-fasta\fR
Write alignments in a FASTA file
.TP
\fB\-\-plot\-only\fR
Run only plotting from a valid result folder
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Disable any output to stdout
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Display progression information during parsing
.TP
\fB\-\-mapdamage\-modules\fR=\fI\,MAPDAMAGE_MODULES\/\fR
Override the system wide installed mapDamage module
.IP
Options for graphics:
.TP
\fB\-y\fR YMAX, \fB\-\-ymax\fR=\fI\,YMAX\/\fR
graphical y\-axis limit for nucleotide misincorporation
frequencies [0.3]
.TP
\fB\-m\fR READPLOT, \fB\-\-readplot\fR=\fI\,READPLOT\/\fR
read length, in nucleotides, considered for plotting
nucleotide misincorporations [25]
.TP
\fB\-b\fR REFPLOT, \fB\-\-refplot\fR=\fI\,REFPLOT\/\fR
the number of reference nucleotides to consider for
plotting base composition in the region located
upstream and downstream of every read [10]
.TP
\fB\-t\fR TITLE, \fB\-\-title\fR=\fI\,TITLE\/\fR
title used for plots []
.IP
Options for the statistical estimation:
.TP
\fB\-\-rand\fR=\fI\,RAND\/\fR
Number of random starting points for the likelihood
optimization  [30]
.TP
\fB\-\-burn\fR=\fI\,BURN\/\fR
Number of burnin iterations  [10000]
.TP
\fB\-\-adjust\fR=\fI\,ADJUST\/\fR
Number of adjust proposal variance parameters
iterations  [10]
.TP
\fB\-\-iter\fR=\fI\,ITER\/\fR
Number of final MCMC iterations  [50000]
.TP
\fB\-\-forward\fR
Using only the 5' end of the seqs  [False]
.TP
\fB\-\-reverse\fR
Using only the 3' end of the seqs  [False]
.TP
\fB\-\-var\-disp\fR
Variable dispersion in the overhangs  [False]
.TP
\fB\-\-jukes\-cantor\fR
Use Jukes Cantor instead of HKY85  [False]
.TP
\fB\-\-diff\-hangs\fR
The overhangs are different for 5' and 3'  [False]
.TP
\fB\-\-fix\-nicks\fR
Fix the nick frequency vector (Only C.T from the 5'
end and G.A from the 3' end)  [False]
.TP
\fB\-\-use\-raw\-nick\-freq\fR
Use the raw nick frequency vector without smoothing
[False]
.TP
\fB\-\-single\-stranded\fR
Single stranded protocol [False]
.TP
\fB\-\-theme\-bw\fR
Use black and white theme in post. pred. plot [False]
.TP
\fB\-\-seq\-length\fR=\fI\,SEQ_LENGTH\/\fR
How long sequence to use from each side [12]
.TP
\fB\-\-stats\-only\fR
Run only statistical estimation from a valid result
folder
.TP
\fB\-\-rescale\fR
Rescale the quality scores in the BAM file using the
output from the statistical estimation
.TP
\fB\-\-rescale\-only\fR
Run only rescaling from a valid result folder
.TP
\fB\-\-rescale\-out\fR=\fI\,RESCALE_OUT\/\fR
Write the rescaled BAM to this file
.TP
\fB\-\-no\-stats\fR
Disabled statistical estimation, active by default
.TP
\fB\-\-check\-R\-packages\fR
Check if the R modules are working
.SH BUGS
Report bugs to aginolhac@snm.ku.dk, MSchubert@snm.ku.dk or
jonsson.hakon@gmail.com
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.