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
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)
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