MIRPIPE specifications

Information


Unique identifier OMICS_09248
Name MIRPIPE
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data miRNAseq
Output data miRNAs with expression
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Carsten Künne

Information


Unique identifier OMICS_09248
Name MIRPIPE
Interface Web user interface
Restrictions to use None
Input data miRNAseq
Output data miRNAs with expression
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Programming languages Perl
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Carsten Künne

Publication for MIRPIPE

MIRPIPE citations

 (2)
library_books

miRNAs Do Not Regulate Circadian Protein Synthesis in the Dinoflagellate Lingulodinium polyedrum

2017
PLoS One
PMCID: 5245829
PMID: 28103286
DOI: 10.1371/journal.pone.0168817

[…] tential miRNAs were used to search for targets in the transcriptome using psRNATarget with an expected value of 2 or less []. To look for miRNAs in common with those in other dinoflagellates, we used MIRPIPE to search for all reported dinoflagellate miRNAs in the 4.9 million cleaned reads [].The domain structure of Dicers and Argoanutes was determined using the conserved domain function of the Bla […]

library_books

Computational Prediction of miRNA Genes from Small RNA Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4306309
PMID: 25674563
DOI: 10.3389/fbioe.2015.00007

[…] MIRPIPE identifies miRNAs through sequence homology (Kuenne et al., ). It collapses duplicate reads and removes those that have only been sequenced few times. It then further collapses sequences that […]

MIRPIPE institution(s)
Group of Bioinformatics; Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
MIRPIPE funding source(s)
Excellence Cluster Cardio-Pulmonary System (ECCPS); MPI for Heart and Lung Research

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