i-mtz / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming

mirtop

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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Cite

http://mirtop.github.io

About

Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928

Read more: http://mirtop.github.io

Installation

Bioconda

conda install mirtop -c bioconda

PIP

pip install mirtop

develop version

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

Quick start

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

Output

The mirtop gff generates the GFF3 adapter format to capture miRNA variations. The output is explained here.

Contributors

• Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)
• Shruthi Bhat Bandyadka (Partners Personalized Medicine, Cambridge MA, USA)