nblocktester

Bioinformatic tool in Perl for detection of miRNA-like small ncRNA-derived fragments using small RNA-seq data.

https://github.com/aimergdiaz/nblocktester

Repository

Bioinformatic tool in Perl for detection of miRNA-like small ncRNA-derived fragments using small RNA-seq data.

README.Rmd

---
title: "NBlockTester: A bioinformatic tool to detect small ncRNA-derived fragments"
author: "Aimer G. Diaz"
output: github_document
bibliography: References.bib
link-citations: true
csl: https://raw.githubusercontent.com/citation-style-language/styles/master/biomed-central.csl
---

## Description of the tool

NBlockTester is a perl code (in proccess to be a cpan module) written by Aimer G. Diaz, with the supervision and comments of Clara Bermudez and Steve Hoffmann. It's an adaptation of the previously developed tool [blockbuster code](https://www.bioinf.uni-leipzig.de/~david/LIFE/LIFE/blockbuster.html) @langenberger2009evidence, which detect blocks of overlapping reads using a gaussian-distribution approach. NBlockTester it's specially adapted for the detection of small ncRNAs fragments derived from longer ncRNAs like tRNAs, rRNAs, snoRNAs, or even mRNAs @tuck2011rna, using mapped small RNA-seq data (bam files) and a set of genomic coordinates which would be used as a search space. The main purpose of the code is to discriminate small fragments (like tRFs -tRNA derived fragments-) who has a miRNA-like expression pattern from background-source expression (the tRNA source), recover in the small RNAseq protocol of sequencing which might be degradation or technical byproducts (@gutierrez2018deteccion,@gutierrez2024systematic). 

## Installation 

By now just download this repository.

## Running with test data

To Run the code with a small test data set, please just run the shell file 

```
bash run.sh

```

Or alternatively directly launch the perl script: 

```
perl nBlock_tester_npv.pl test_data/Transcribed-non-protein-genes_regions/ncRNA-or-intergenic_regions.bed  test_data/Mapped_tag_reduced_data/12d4_S7.mapped.ncRNA.bam

```

## Dependencies 

The code it's also written to be run in parallel (fork), however it does requires the cpan module "Parallel::ForkManager". To install this module just run: 

```
cpan upgrade Test::More

cpan Parallel::ForkManager

```

Test installation by running 

```
perl -e 'use Parallel::ForkManager;'
```

To run parallel version of the code just assing the number of threads to be use: 
```
perl nBlock_tester.pl  2  test_data/Transcribed-non-protein-genes_regions/ncRNA-or-intergenic_regions.bed  test_data/Mapped_tag_reduced_data/12d4_S7.mapped.ncRNA.bam
```

## License 

The code is freely available to download and run, but it's protected and licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](https://creativecommons.org/licenses/by-nc/4.0/), meaning you can use it but citing it's source. 

[![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)

## Cite

This code is cited and published on @gutierrez2024systematic

## Viewers 

[![Image of Viewers](https://github.com/AimerGDiaz/Viewers/blob/master/svg/409164432/badge.svg)](https://github.com/AimerGDiaz/Viewers/blob/master/readme/409164432/week.md)

## References 

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Gutierrez-Diaz"
  given-names: "Aimer"
  orcid: "https://orcid.org/0000-0002-0179-7627"
title: "NBlockTester"
version: 0.1
doi: 	10.13140/RG.2.2.29837.08162
date-released: 2018-09-14
url: "https://github.com/AimerGDiaz/NBlockTester"

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