TEannot Lite

Description

REPET is for detection and annotation of transposable elements (TE). The ligth version available on Galaxy is specialised on transposable element masking. TEannot is the second and last step to mask TE on the genome. For a detailed description of each parameter used, please consult the Galaxy page in "Shared Data > Published Pages"

Workflow position

Upstream tools

Name	output file(s)	format
TEdenovo	Fasta file with TE library	fasta

Input file

Fasta file: Genome file at fasta format
Library file: Fasta file with a library of transposable elements from TEdenovo.

Parameters

Masked file: To get an additionnal output file : Masked fasta file

Output files

Output_gff3: GFF3 file with transposable elements
Output_masked_fasta: Input fasta file masked with TE infos
Output_config: File to show which params have been used
Output_stats: File with statistics on TE library

Dependencies

Working example

Input files

Fasta file

>dmel_chr4
GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGAAAGTAATACTAATCCATGACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA

Fasta Library

>DTX-incomp_20150325110123-B-G1-Map3
ATACAGCTGCGGTTAAAATAATAGCACTACTGCAGGTGGAAAGTTGATTTCCTAAAAAAA
ATTATTAAATGTTTATATTTTTTTAAGTCAGATTGCATGAATAATAAGTACCATATGTTG
GCTCTCTGAGCAAGAAATTTTTAGTCTCT
>DTX-incomp_20150325110123-B-P1.0-Map3
CTTGTGTCCGCACTTCGTGCCTCAAGATATGAACAAAGCAAAGACACTAGAATAATTCTA
GTGTATTACTTTGATATTACTTTTGCAATAAACAGTTATCATATTTTTA

Output files

GFF3 output :

##gff-version 3
dmel_chr4       test_REPET_TEs        match   971161  971469  0.0     -       .       ID=ms1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Target=DTX-incomp_DmelChr4-B-G1-Map3 45 542
dmel_chr4       test_REPET_TEs        match_part      971161  971271  0.0     -       .       ID=mp1-1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Parent=ms1_dmel_chr4_DTX-incomp_DmelChr4-B-G1-Map3;Target=DTX-incomp_DmelChr4-B-G1-Map3 435 542;Identity=94.4

Masked fasta output :

>dmel_chr4
GAGAACCGTCCTGTAAGTACTCTTGCTTTAAATACGXXXXXXXXXXXXXXXXXXXXACGCTTAAGTCGAAGAGAGAATAAGTCAATATTTAATTGGACTCATCGCTTATGTTCATCATGAATCTATAGTTAACTTGATGTTGTGCTCCATGTACGATATAAAAAGTTAGATA

Config file :

[repet_env]
repet_version: 2.4
repet_host: ******
repet_user: ******

Statistics file :

nb of sequences: 8
nb of matched sequences: 8
cumulative coverage: 133656 bp