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GFF3 format with miRNA and isomiR information from sequencing data
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readme.md

A proxy for miRNA/isomiR data analysis where all tools meet with the idea to create an ecosystem of data analysis promoting community collaboration.

Project Status: Active – The project has reached a stable, usable state and is being actively developed. Description example FAIR EDAM biorxiv

Introduction

As discussed here: https://github.com/miRTop/incubator/issues/10 we've defined a GFF3 format for output of small RNA pipelines focused on miRNA data currently. We is an open community project (read more) and joint us!

This output is based on the current GFF3 definition: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

Note: Keep in mind this is for the output of a pipeline, so we know there will be bias toward methodology, but the idea is to put enough information to be able to re-analyze or filter sequences using information described here. As well, it would be a proxy for downstream analysis or packages.

Advantages

  • Developers of miRNA detection and annotation tools can open their results to other tools and communities using this format.

  • Developers of downstream analysis can use the output from any supported annotation tool to work on variant calling, visualization, filtering, ensemble strategy to call isomiRs, etc ...

If you want to fo fast, go alone; If you want to go far, go together

by Tracy Teal (Data Carpenter CEO, GCC BOSC 2018) see slides

Version

VERSION: 1.2

Contact

miRTop group

Authors: @lpantano @gurgese @ThomasDesvignes @mhalushka @mlhack @keilbeck @BastianFromm @ivlachos @TJU-CMC @sbb25

Share any questions and/or suggestions

Compatible tools

  • miRGe2.0
  • bcbio - seqbuster(miraligner)
  • sRNAbench
  • isomiR-SEA
  • PROST!
  • isomiRs

Make your tool compatible, open an issue today!

TOOL

We have created mirtop to help with the format:

  • Convert to GFF
  • Convert from GFF
  • Validator

Link to the tool: https://mirtop.readthedocs.io/en/latest/

Implementation

Presentations

Note: if you presented this work, please chime in this issue # TODO missing link

Reference

1: Desvignes T, EIlbeck K, S. Vlachos I et al. miRTOP: An open source community project for the development of a unified format file for miRNA data [version 1; not peer reviewed]. F1000Research 2018, 7(ISCB Comm J):953 (slides) (doi: 10.7490/f1000research.1115724.1)

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