Ub-ISAP specifications

Information


Unique identifier OMICS_19200
Name Ub-ISAP
Alternative name UNIX-based vector Integration Site Analysis Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Multiple raw next-generation sequencing (NGS) reads in a single (single reads or paired-end reads), the 5′ TR primer and the 3′ distal primer sequences used in library preparation.
Input format FASTQ
Output data Chromosomal positioning, closest gene accession number, symbol from the processed reads in, and the unique ISs characterized as transcription start site (TSS) proximal, intragenic or intergenic.
Output format Tabular format as.txt file
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements cutadapt, Bowtie2, Bedtools
Maintained Yes

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Maintainer


  • person_outline Atul Kamboj <>

Publication for UNIX-based vector Integration Site Analysis Pipeline

Ub-ISAP institution(s)
Children’s Cancer Research Unit, Kid’s Research Institute, The Children’s Hospital at Westmead, Westmead, NSW, Australia; Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Westmead, NSW, Australia; The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, NSW, Australia; Cancer Centre for Children, The Children’s Hospital, Westmead, NSW, Australia
Ub-ISAP funding source(s)
Supported by The Kid’s Cancer Project.

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