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Introduction

Transgene

A transgene is genetic material transferred to a host genome by genetic engineering techniques, either by (1) integration by insertion or (2) integration by homologous recombination.

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The transgene detection functions described here are designed to identify transgene integration. The workflow reports a list of detected transgene integration sites, statistics of supporting reads, as well as genomic locations of breakpoints, which characterize transgene sites comprehensively at base-pair resolution. Alignment files (NgsData) will also be generated to visualize transgene events in the genome browser, and variation detection of the product.

Test Dataset

Download link: http://omicsoft.com/downloads/data/Tutorial/Transgene.zip

The test data contains files below

  • Plasmid reference sequence in FASTA format
  • Plasmid gene model in GTF format.
  • Plasmid gene location in BED format
  • 2x100bp paired end fastq.gz files containing NGS reads from regions surrounding the transgene.

It is a semi-simulated dataset mimicking enrichment of transgene regions using pull down techniques.