MAPDAMAGE(1)

✨ NAME ✨

mapDamage — tracking and quantifying damage patterns in ancient DNA sequences 💀🧬

okay so first things first: this is a User Command, manual section 1, and it's literally the whole plot — you hand it ancient DNA, it counts up the damage. iconic.

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🌸 SYNOPSIS 🌸

mapDamage [options] -i BAMfile -r reference.fasta

like, give it a BAM and a reference and let it cook 💅

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🦋 DESCRIPTION 🦋

MapDamage is a computational framework written in Python and R, and what it does is track and quantify DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. no cap. that's the whole job and it does it beautifully 🫶

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💅 OPTIONS 💅

okay bestie, here's the menu. every single flag, nothing skipped, we're not doing that 🙈

• --version — show program's version number and exit
• -h, --help — show this help message and exit

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🎀 Input files 🎀

the ones you literally cannot skip, fr fr

• -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

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🌈 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. (so like, do nothing and it just reads everything, your call ✨)
• --downsample-seed=DOWNSAMPLE_SEED — Seed value to use for downsampling. See documentation for py module 'random' for default behavior.
• --merge-reference-sequences — Ignore reference sequence names when tabulating reads (using '*' instead). Useful for alignments with a large number of reference sequences, which may otherwise result in excessive memory or disk usage due to the number of tables generated. (translation: lots of refs = lots of tables = your disk crying 😭)
• -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

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🎨 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 []

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🔥 Options for the statistical estimation 🔥

this is the main character section, ngl

• --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

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💀 BUGS 💀

found a bug? do NOT suffer in silence bestie, report it:

• aginolhac@snm.ku.dk
• MSchubert@snm.ku.dk
• jonsson.hakon@gmail.com

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👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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and that's the whole page, bestie 💖 this was mapDamage 2.0.6, dated August 2016, living in section 1 of the manual (the User Commands one, iykyk). go forth and quantify some damage, you absolute icon 🧬✨🎀