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Small RNA-seq annotation

Project 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

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 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 and the last one will have the ID name for the isomiR, 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.sGT.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).

See [here](https://github.com/miRTop/incubator/blob/master/isomirs/isomir_naming.md#examples) for more examples.

Use [isomiRs R package for the analysis](http://bioconductor.org/packages/3.5/bioc/html/isomiRs.html)

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