Aimer G. Diaz
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 [1], 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 [2], 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 ([3],[4]).
By now just download this repository.
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
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
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, meaning you can use it but citing it’s source.
This code is cited and published on [4]
1. Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics. 2009;25:2298–301.
2. Tuck AC, Tollervey D. RNA in pieces. Trends in genetics. 2011;27:422–32.
3. Gutiérrez Dı́az AA. Detección automatizada de pequeños fragmentos derivados de RNAs no-codificantes expresados diferencialmente frente a la infección del virus dengue. 2018.
4. Gutierrez-Diaz A, Hoffmann S, Gallego-Gómez JC, Bermudez-Santana CI. Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells. Frontiers in Bioinformatics. 2024;4:1293412.