Metadata-Version: 1.1
Name: mirtop
Version: 0.1.2a
Summary: Small RNA-seq annotation
Home-page: http://github.com/lpantano/mirtop
Author: Lorena Pantano
Author-email: lpantano@iscb.org
License: MIT
Description: mirtop
        ---------
        
        ![](https://travis-ci.org/lpantano/seqcluster.png?branch=master)
           
        
        Command line tool to annotate with a standard naming miRNAs e isomiRs.
        
        See more at: [isomiRs naming discussion](https://github.com/miRTop/incubator/blob/master/isomirs/isomir_naming.md)
        
        Cite
        ---------
        
        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 annotate --sps hsa --hairpin examples/annotate/hairpin.fa --mirna examples/annotate/miRNA.str -o test_out_mirs_fasta examples/annotate/sim_isomir.fa`
        
        Output
        ------
        
        There will be a `*.mirna` file that is a tabular file with this format:
        
        ![](docs/figures/output.png)
        
        Naming of isomiRs follow these rules:
        
        * Changes at 5' end: ``0/NA`` means no modification. ``UPPER CASE LETTER`` means nucleotide insertions (sequence starts before miRBase mature position). ``LOWWER CASE LETTER`` means nucleotide deletions (sequence starts after miRBase mature position).
        * Changes at 3' end: ``0/NA`` means no modification. ``UPPER CASE LETTER`` means nucleotide insertions (sequence ends after miRBase mature position). ``LOWWER CASE LETTER`` means nucleotide deletions (sequence ends before miRBase mature position).
        * Additions at 3' end: ``0/NA`` means no modification. ``UPPER CASE LETTER`` means addition at the end. Note these nucleotides don't match the precursor. So they are post-transcriptional modification.
        * Nucleotide substitution: ``NUMBER|NUCLEOTIDE_ISOMIR|NUCLEOTIDE_REFERENCE`` means at the position giving by the number the nucleotide in the sequence has substituted the nucleotide in the reference. This, as well, is a post-transcriptional modification.
        
        There are two different outputs right now: 1) tab limited format, where each column will refer to the previous 4 points, or 2) a merged format, where these 4 points (mirna, substitution, addition, 5 trimming, 3 trimming) are separated by ``:``. For instance: ``hsa-let-7a-5p:0:0:GT:t`` means ``hsa-let-7a-5p`` has a 5' trimming event (starts 2 nts before the reference miRNA) and a 3' trimming event (ends 1 nt before the reference miRNA).
        
        
        Use [isomiRs R package for the analysis](http://bioconductor.org/packages/3.5/bioc/html/isomiRs.html)
        
        Contributors
        ------------
        
        * [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
        
        
Keywords: RNA-seq miRNA isomiRs annotation
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
