ExInAtor specifications


Unique identifier OMICS_15528
Name ExInAtor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data ExInAtor requires eight mandatory inputs: (1) a gene annotation in GTF format containing information on genes and exons to analyse (transcript information is ignored), (2) a catalogue of mutations in BED format, (3) the number of individual genomes or samples represented by the BED file, (4) the output folder destination, (5) a file with two columns showing the name of each chromosome and its nucleotide length, (6) a gene annotation in GTF format containing information on genes and exons of the whole genome (transcript information is ignored), (7) FASTA file of the whole genome and (8) a file containing all the possible trinucleotides.
Input format GTF, BED, FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
Computer skills Advanced
Stability Stable
Requirements Bedtools, Awk
Maintained Yes



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  • person_outline Rory Johnson <>

Publication for ExInAtor

ExInAtor funding source(s)
This work was supported by the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017′, SEV-2012-0208, Ramón y Cajal RYC-2011-08851, Plan Nacional BIO2011-27220, a pre-doctoral fellowship FPU14/03371 and the NCCR RNA & Disease funded by the Swiss National Science Foundation.

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