Command line tool to annotate with a standard naming miRNAs e isomiRs.
This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/mirGFF3
Ask question, ideas Contributors to code
Everybody is welcome to contribute, fork the devel branch and start working!
If you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:
https://github.com/miRTop/incubator/issues
Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
Read more: http://mirtop.github.io
conda install mirtop -c bioconda
pip install mirtop
Thes best solution is to install conda to get an independent enviroment.
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$PATH:~/mirtop_env
conda install -c bioconda pysam pybedtools pandas biopython samtools
git clone http://github.com/miRTop/mirtop
cd mirtop
python setup.py develop
Read complete commands at: https://mirtop.readthedocs.org
git clone mirtop
cd mirtop/data/examples/annotate
mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam
The mirtop gff generates the GFF3 adapter format to capture miRNA variations. The output is explained here.
- Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
- Shruthi Bhat Bandyadka (Partners Personalized Medicine, Cambridge MA, USA)
- Iñaki Martínez de Ilarduya(HPC core, IGTP, Badalona, Spain)
- Rafael Alis
- [Victor Barrera]((https://github.com/vbarrera) (Bioinformatic Core, Harvard Chan School, Boston, USA)
- Steffen Möller (University of Rostock)