Genome Mappability Track Instant Analysis

What is mappability?

Mappability is a genome-wide function showing if a region in a genome could be identified unambiguously using a read of a particular length. This function typically ranges between 0 and 100. If exact genome subsequence may be found in more than one location, then the mappability in that location of the genome is set to zero. Otherwise, if the subsequence is unique, mappabity is close to 100.

Obviously, mappability depends on read length (the more read length the more unambiguous locus is), and insertion size for paired-end reads (growing of insertion size improves mappability as well).

Quick Start

Installation (for Python3)

pip3 install --user git+https://github.com/bioinf/Gematria numpy pyBigWig
curl https://raw.githubusercontent.com/bioinf/Gematria/master/gematria.standalone.py > gematria.py
chmod +x gematria.py

Usage

./gematria.py [fasta file] [Optional arguments]

Optional arguments

-l, --length   Read length. Default: 100
-t, --threads  Number of threads. Default: auto
-o, --output   Output formats: [wig],bigwig,bed,tdf,bigbed,all
-p, --paired   To use paired end reads, specify the insert size
               and the standard deviation (normal distribution model)
               If you don’t know where to start, use -p 300,100
-m, --lowmem   Use the RAM-memory saving algorithm. Default: none
                 -m hard / will be used ~ 5 × Genome Size
                 -m soft / will be used ~ 7 × Genome Size
               Specifying this parameter in the value hard or soft 
               makes it impossible to use multithreading.
-h, --help     Show this help
-v, --version  Show version number

Examples:

Run with default parameters

./gematria.py ./test/example.fa

Read size determination -l 20

./gematria.py ./test/example.fa -l 20

By default, the result is saved to the .wig file. You can specify additional export formats -o all

./gematria.py ./test/example.fa -o bigbed
./gematria.py ./test/example.fa -o bigwig,bed,tdf
./gematria.py ./test/example.fa -o all

The default mappability calculation is for single-end reads -p S.

For paired reads, you can specify the insert size. For example, if the insert size is normally distributed with an average = 30 and sigma = 10, use the following parameter: -p 30,10

./gematria.py ./test/example.fa -p 30,10

Inside the program there are two ways to calculate mappability track. If you want to use exactly the approach with Filters, specify -m hard or -m hard This approach saves memory but does not have a multithreaded run.

./gematria.py ./test/example.fa -m hard

If you want to use the QuickSort-approach, specify number of threads -t 16

./gematria.py ./test/example.fa -t 16

Installation without a superuser

if you are working on a shared server, and you do not have root access, you can locally install the python and the required extensions as follows:

Python3, pip, Packages

git clone https://github.com/python/cpython.git
cd cpython && git checkout origin/3.7

./configure --with-pydebug && make -j && cd ../
wget https://bootstrap.pypa.io/get-pip.py

./cpython/python get-pip.py --user
./cpython/python .local/bin/pip3.7 \
  install --user git+https://github.com/bioinf/Gematria numpy pyBigWig

Gematria

curl https://raw.githubusercontent.com/bioinf/Gematria/master/gematria.standalone.py > gematria.py
./cpython/python gematria.py

Development

git clone https://github.com/bioinf/Gematria.git ./gematria
cd gematria

Quick tests

Run gematria with different parameters:

python3 ./test/gematria.test.py

Gematria.py

The script uses the contents of the folder /include and auxiliary applications from the /exe folder. If you find it convenient to compile all the code into one script (gematria.standalone.py) and use it, run the command:

python3 build.py && chmod +x gematria.standalone.py