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