Does miRDeep2.pl module support multi-thread? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Does miRDeep2.pl module support multi-thread?

I am currently using the miRdeep2 module to predict novel miRNAs. However, I noticed that the '#computing rnandfold p-values' process took a very long time. I wonder if I can accelerate the process by enabling multithreaded calculation? It seems there is no such option for miRDeep2.pl: https://github.com/rajewsky-lab/mirdeep2/blob/master/README.md

Any ideas?

mirna rna-seq srna mirdeep2 srna-seq

• 223 views • link

updated 6.6 years ago by zubenel

• written 6.6 years ago by 2822462298 •

1 answer

You are right as there is no option for running miRDeep2.pl by enabling multithreading. If you know Perl well enough you could study miRDeep2.pl script in order to find out if it is worth it to try incorporate multithreading. If you follow this route you may find Perl tutorial on threads useful.

• 0 views • link

written 6.6 years ago by zubenel

Thank you! Will try.

• 0 views • link

written 6.6 years ago by 2822462298 •

Log in to answer this question.

More posts like this

Job: Bioinformatics Analyst - Laboratory Medicine and Pathology
written 2.0 years ago by toddknutson

**Laboratory Medicine and Pathology Bioinformatics Analyst (Researcher 5 - 9742R5)** **About the Position** The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing …
Tool: Just released VEBA 2.0 in Nucleic Acids Research, a modular genome-resolved metagenomics/meta…
written 2.1 years ago by O.rka

![enter image description here][1] I've been developing the VEBA software suite during the beginning of COVID lockdown. Had a 2022 release in BMC Bioinformatics for …
Job: Bioinformatics Analyst - Laboratory Medicine and Pathology
written 2.3 years ago by toddknutson

**Laboratory Medicine and Pathology Bioinformatics Analyst (Researcher 5 - 9742R5)** **About the Position** The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing …
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Plea…
written 2.3 years ago by AdviceSeeker •

I'm seeking guidance on how to get out of a situation I'm currently in. After reporting my former supervisor's spouse for discriminatory harassment, I've experienced …
Job: PhD fellowship in computational CRISPR guide RNA design
written 3.1 years ago by info

Faculty of Health and Medical Sciences University of Copenhagen A PhD fellowship is available in the Computational Biology and Bioinformatics research group (http://ivh.ku.dk/bioinformatics), Center for …
miRDeep2 Support
written 5.4 years ago by VineethVenumadhavan •

Dear Biostars, Appreciate your support regarding miRNA bioinformatics analysis with miRDeep2. Otherwise please redirect me to an expert / forum to which I can raise …
Several questions about miRDeep2
written 6.6 years ago by 2822462298 •

Hi all, I am currently using miRDeep2 to identify miRNAs in a non-model organism (a butterfly). After running mapper.pl to map the small RNA reads …
How to integrate mirdeep2 result from different samples
written 6.9 years ago by Ziliang Luo •

Hello, I'm using mirdeep2 to analyze my small RNA seq data (50 bp). I followed their tutorial for the analysis:https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md. I analyzed each sample separately …
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
written 9.7 years ago by Brian Bushnell

I'd like to introduce a new member of the [BBMap][1] package, **Clumpify**. This is a bit different from other tools in that it does not …