Cmake is needed for installation (CMAKE). You can download it directly from http://www.cmake.org/cmake/resources/software.html or use an appropriate packet manager. In the following instructions we show the procedure to install, compile and run CHESTER:
Download, install and resolve conflicts.
sudo apt-get install cmake git clone https://github.com/pratas/chester.git cd chester/src/ cmake . make
Alternatively, you can install (without cmake and git, but only for linux) using
wget https://github.com/pratas/chester/archive/master.zip unzip master.zip cd chester-master/src/ mv Makefile.linux Makefile make
Install brew:
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
only if you do not have it. After type:
brew install cmake brew install wget brew install gcc48 wget https://github.com/pratas/chester/archive/master.zip unzip master.zip cd chester-master/src/ cmake . make
With some versions you might need to create a link to cc or gcc (after the brew install gcc48 command), namely
sudo mv /usr/bin/gcc /usr/bin/gcc-old # gcc backup sudo mv /usr/bin/cc /usr/bin/cc-old # cc backup sudo ln -s /usr/bin/gcc-4.8 /usr/bin/gcc sudo ln -s /usr/bin/gcc-4.8 /usr/bin/cc
In some versions, the gcc48 is installed over /usr/local/bin, therefore you might need to substitute the last two commands by the following two:
sudo ln -s /usr/local/bin/gcc-4.8 /usr/bin/gcc sudo ln -s /usr/local/bin/gcc-4.8 /usr/bin/cc
In windows use cygwin (https://www.cygwin.com/) and make sure that it is included in the installation: cmake, make, zcat, unzip, wget, tr, grep (and any dependencies). If you install the complete cygwin packet then all these will be installed. After, all steps will be the same as in Linux.
Run CHESTER-map:
./CHESTER-map -v -k 30 -i -s 6099999999 File1.fastq:File2.fastq:File3.fasta FileA.fasta:FileB.fasta
To see the possible options type
./CHESTER-map
or
./CHESTER-map -h
These will print the following options:
Usage: CHESTER-map <OPTIONS>... [FILE]:<...> [FILE]:<...> CHESTER-map: a tool to map relative singularity regions The (probabilistic) Bloom filter is automatically set. -v verbose mode, -a about CHESTER, -s <value> bloom size, -i use inversions, -p show positions/words, -k <value> k-mer size (up to 30), [rFile1]:<rFile2>:<...> reference file(s), [tFile1]:<tFile2>:<...> target file(s). The reference files may be FASTA, FASTQ or DNA-SEQ, while the target files may be FASTA or DNA-SEQ. Report bugs to <{pratas,ap,pjf}@ua.pt>.
Most of the values are set automatically.
For CHESTER-filter type:
./CHESTER-filter
while for CHESTER-visual type:
./CHESTER-visual
The following illustrate a Human-Neanderthal example. For the purpose go to the base and run:
cp ancient/runNeanderthalGRC37.sh . . RunNeanderthalGRC73.sh &
It will download all the sequences and run CHESTER-map. This will output the plot.svg, with the human novel regions relatively to the Neanderthal, chromosome by chromosome. The next image illustrate such result:
On using this software/method please cite:
D. Pratas, M. Hosseini, R. M. Silva, A. J. Pinho, P. J. S. G. Ferreira. Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome. Iberian Conference on Pattern Recognition and Image Analysis. Springer, Cham, 2017.
D. Pratas, R. M. Silva, A. J. Pinho, P. J. S. G. Ferreira. Detection and visualisation of regions of human DNA not present in other primates. Proceedings of the 21st Portuguese Conference on Pattern Recognition, RecPad 2015, Faro, Portugal, October 2015.
For any issue let us know at issues link.
GPL v3.
For more information:
http://www.gnu.org/licenses/gpl-3.0.html