FineSplice specifications

Information


Unique identifier OMICS_03274
Name FineSplice
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for FineSplice

FineSplice citations

 (2)
library_books

A Developmental Transcriptome Map for Allotetraploid Arachis hypogaea

2016
Front Plant Sci
PMCID: 5043296
PMID: 27746793
DOI: 10.3389/fpls.2016.01446

[…] Reads were mapped to a concatenated A. ipaensis and A. duranensis genome (Bertioli et al., ; peanutbase.org; pseudomolecules v1.0) using Tophat2 v. 2.1.0 (Kim et al., ). Finesplice (Gatto et al., ) was then used to identify all splice junctions present in the data. Any splice junctions that were not supported by at least 10 reads in a single sample were filtered out. […]

library_books

Computational Identification of Novel Genes: Current and Future Perspectives

2016
Bioinform Biol Insights
PMCID: 4970615
PMID: 27493475
DOI: 10.4137/BBI.S39950

[…] ce site predictor based on multiple sequence alignments is SPLICEVIEW, whereas NetGene2 uses a neural network approach. Splice site prediction can be achieved using RNA-seq data with the KisSplice or FineSplice tools. The RSVP tool predicts splice variants of genes based on a genomic sequence and incorporates information from RNA-seq reads. A comparison of computational effort and dependency to bi […]

FineSplice institution(s)
Cardiovascular Development and Repair Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain; Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain; National Heart and Lung Institute, Imperial College London, London, UK; Cardiovascular Biomedical Research Unit, NIHR Royal Brompton and Harefield NHS Foundation Trust, London, UK; Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore; Cardiovascular and Metabolic Disorders Program, Duke-NUS Graduate Medical School, Singapore, Singapore

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