TIDAL1.2 Documentation

For code visit GitHub

About TIDAL1.2

TIDAL is pipeline built to identify Transposon Insertion and Depletion in flies. The pipeline uses shell scrips, PERL, C and a combination of other publicly available tools. TIDAL uses a split read approach to identify Transposon Insertion and Depletion sites, and addition steps are implemented to reduce false positives.

TIDAL1.2 includes a few additional features

• Incorporation of IGEs (Immobile Genetic Elements) and tracking there insertion/deletion frequency

• Generate counts for transposon as proxy for copy number (not part of the default TIDAL output)

• update dependencies for the pipeline

Features

• Flexible (TIDAL can be run with SRA files, Paired End and Single End libraries)

• Annotation Rich (TIDAL outputs have detailed annotation)

• Increased Specificity (Less false positives in outputs)

• Calculate coverage ratio to determine heterogenity of sites

Contents

• Installation
  • Software Dependencies
  • Source Code
  • Annotation Files
  • Compile C code
  • Update Shell Scripts
• Run
  • TIDAL from SRA
  • TIDAL from fastq
  • Outputs
• Outputs

Support

Please use Github issues to bring up any errors that occur with software.

License

The project is licensed under the BSD license.

Acknowledgement

Thanks to David Tang for his blat parser script (psl_to_bed_best_score.pl)