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/incubator/blob/master/format/definition.md
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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/example/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)