Introduction to transposable element detection using sequencing data

• Introduction to the Linux Operating System
  • First contact with the shell (Bash Terminal)
  • Basic command lines
  • File system (ftp/ssh protocols)
  • Text editors (emacs, notepad)
  • Working with text files with commands such as grep, sed , tr and awk

• Introduction on TE biology
  • TE discovery
  • TE classification

• Enforcement to solve common problems in bioinformatics
  • Analysis of sequences – Fasta format
  • Look for particular patterns in TE sequences ( LTR, TIR or TSD)
  • Parsing common annotation files (gff,bed,vcf)Tuesday, June 15th, 2019

• How to detect TE in assembled genomes?
  • Annotation of TE families using de novo approaches
  • Detection and annotation of individual TE insertions

• Application by group: TE annotation in Drosophila
  • RepeatMasker presentation and command line
  • How to interpret the RepeatMasker outputs
  • How to parse the RepeatMasker output (OneCodeTofindThemAll)

• Each group present their RepeatMasker results

• Introduction to the next-generation sequencing
  • Sequencing technologies
  • Sequencing data – Fastq format

• Discussions : Not all TE insertions are part of the assembly?

• Application by group: TE families detection in Drosophila
  • DNAPipeTE presentation and command line
  • How to interpret the DNAPipeTE outputs

• Each group present their own results

• Sequencing projects – Population genomics projects: case of DGRP

• Presence/absence calls of previously detected TE insertions
  • T-lex presentation and command line
  • How to interpret the T-lex output
•  Each group present their own results

• Do not forget the novel TE insertions
  • General approach
  • McClintock presentation and command line
  • How to interpret the McClintock output

• Application by group: de novo TE detection in Drosophila using DGRP data

• Each group present their own results

• The advantages of the long-read sequencing technology

• Questions

Participants must have a personal computer (Windows, Mac, Linux) and access to a good internet connection. The use of a webcam and headphones is strongly recommended.

Participants should be familiar with Bash and the use of command lines.