Ub-ISAP specifications

Unique identifier:
OMICS_19200
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTQ
Output format:
Tabular format as.txt file
Programming languages:
Perl
Stability:
Stable
Maintained:
Yes
Name:
UNIX-based vector Integration Site Analysis Pipeline
Interface:
Command line interface
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.
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.
Operating system:
Unix/Linux
Computer skills:
Advanced
Requirements:
cutadapt, Bowtie2, Bedtools

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Ub-ISAP distribution

download

Ub-ISAP support

Maintainer

  • Atul Kamboj <>

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Publications

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

Funding source(s)

Supported by The Kid’s Cancer Project.

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