mapDamage is a Perl script that tracks DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
News in version 0.3.3
- Bug correction: for mapped reads close to the reference ends, we were asking for nucleotides out of range due to the around option.
- Add the -c option to map step to chain all the three steps (map, merge, plot) until generating the pdf. Thus add the options -b, -y and -m at the map step to control the plot range.
- BEDtools version 2.15 changed its version output, resulting in mapDamage to stop. BEDtools checking was disabled.
- BAM files can be used as inputs just as like SAM files.
- In the results folder, two new tables are written: 5pCtoT_freq.txt and 3pGtoA_freq.txt that display the frequencies for -l positions of C>T at 5'-ends and G>A at 3'-ends. respectively.
In addition to the mapDamage Perl script, SAMtools, BEDtools and R are mandatory and must be present in your $PATH. Click here to download SAMtools, here to download BEDtools and here for R.
Three main commands can be used: map, merge and plot. The -c option in map allows to chain all the three steps. A detailed description is presented below:
The detailed manual page can be found associated here with version 0.3.2.
- 1. map
./mapDamage-0.3.3.pl map -i input_SAM -d directory -r reference_fasta -c -t my_title
- -i : input SAM-file without header. SAM format, version 1.4 is described in this pdf file
- -r : input reference fasta file, with headers identical to the ones in the input_SAM file
- -l : maximal read length, in nucleotides to consider [default: 70]
- -a : size, in nucleotides, of the genomic region to be retrieved before and after reads [default: 10]
- -d : folder for writing output-files, if not already present, this folder will be automatically created [default name: results_input_SAM.filtered]
- -j : second input SAM-file without header; reads present in both SAM files will not be processed
- -u : removes all non-unique reads based on the X1 and XT tags from the BWA mapper
- -k : keep bed file and fasta file containing all the genomic regions [default: delete these files]
- -f : outputs all read aligned against the reference genome, in a fasta file format
- -c : complete analysis, map will be automatically followed by both merge and plot steps [default: not active]
when -c is active, the following are available to control the plot step:
- -b : the number of reference nucleotides to consider for ploting base composition in the region located upstream and downstream of every read [default: 10]
- -y : graphical y-axis limit for nucleotide misincorporation frequencies [default: 0.30]
- -m : read length, in nucleotides, considered for plotting nucleotide misincorporations [default: 25]
./mapDamage-0.3.3.pl merge -d directory
- -d : folder with output-files generated by the map command
- -c : complete analysis, merge will be automatically followed by the plot step [default: not active]
./mapDamage-0.3.3.pl plot -d directory
- -d : folder with output-files generated by the merge command
- -l : read length, in nucleotides, considered for plotting nucleotide misincorporations [default: 25]
- -m : graphical y-axis limit for nucleotide misincorporation frequencies [default: 0.30]
- -a : the number of reference nucleotides to consider for ploting base composition in the region located upstream and downstream of every read [default: 10]
- -t : title used for both graph and filename [default: folder name without extension]
If you use this script, please cite the following publication:
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
The original version mapDamage-0.2 is still available here.The associated manual page is here.
The positions used in fragmentation files are not compatible with read length > 99999 nucleotides. This is compatible with all sequencing technologies currently available.
Please report bugs and suggest possible improvements to Aurelien Ginolhac by email.