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This excludes extreme insert sizes from small numbers of PE read pairs,
that would otherwise result in the distribution getting pushed into the
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README.md

mapDamage

install with bioconda Conda

Conda Conda Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.

bioconda installation

  • python3 version 2.2.1
conda install -c bioconda mapdamage2=2.2.1
  • python3 version 2.2.1 with R and 4 mandatory packages for the Bayesian inference:
conda install -c bioconda mapdamage2=2.2.1=pyr40_0

Important

  • From version 2.2.1 the master branch is requiring python3 as python2 is not supported from 2020-01-01.

  • Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of mapDamage to use half of the data for estimation of the damage parameters, sorry for the inconvenience.

Introduction

Complete documentation, instructions, examples, screenshots and FAQ are available at this address.

mapDamage2 is a computational framework written in Python3 and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

mapDamage was developed at the Centre for GeoGenetics by the Orlando Group .

Citation

If you use this program, please cite the following publication: Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193

The original mapDamage1 was published in the following article: Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011 27(15):2153-5 http://bioinformatics.oxfordjournals.org/content/27/15/2153

Test the no-stats part and rescaling

you can test mapDamage by running:

cd mapDamage/mapdamage/
python3 mp_test.py

should return

Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats
	Reading from 'tests/test.bam'
	Writing results to 'tests/results/'
pdf tests/results/Fragmisincorporation_plot.pdf generated
additional tests/results/Length_plot.pdf generated
Successful run
.
----------------------------------------------------------------------
Ran 2 tests in 3.357s

OK

Contact

Please report bugs and suggest possible improvements on GitHub: https://github.com/ginolhac/mapDamage/issues/new

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