MGcount is a program for counting whole-transcriptome RNA-seq reads from one or more input alignment files (.bam). It is specially designed to incorporate multi-mapping and multi-overlapping reads in the quantification using a flexible methodology that is compatible with any biotype. At the end of its execution, it produces a count matrix, compatible with any downstream analysis.

MGcount deppends on FeatureCounts. Please download it from the following link: http://subread.sourceforge.net/

MGcount is written in Python and is executed from the command line. You can either download the executable version (single binary file) or install it as a Python3 module.

You can install the package as a Python module:

pip3 install git+https://github.com/hitaandrea/MGcount.git

Once the package is installed, run the tool as a Python installed module:

python3 -m mgcount [args]

Alternatively can download the latest release as a binary executable file here.

Save the program file to your Linux system and set the permissions to allow executing the file as program:

chmod +x mgcount

Once the file is executable, run the tool by calling the file from the command line with the desired arguments.

MGcount [args]

MGcount user guide can be found inside the docs subfolder or accessed through the following link: Link to User Guide!

The work is funded by a Marie Curie early stage researcher fellowship. (European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 813282).

MGcount itself is free software distributed under GPL.

For more details, please, check our paper! https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04544-3