mirtop

Command line tool to annotate with a standard naming miRNAs e isomiRs.

See more at: isomiRs naming discussion

Cite

http://mirtop.github.io

About

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

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

Installation

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

git clone http://github.com/miRTop/mirtop

cd mirtop

python setup.py develop

Quick start

cd data `mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --mirna examples/annotate/hsa.gff3 -o test_out_mirs_fasta examples/annotate/sim_isomir.sam

Output

There will be a *.mirna file that is a tabular file with this format:

Naming of isomiRs follow these rules: https://github.com/miRTop/incubator/blob/master/format/definition.md

Contributors

• Lorena Pantano (Bioinformatic Core, Harvard Chan School, Boston, USA)