TEdenovo Lite

Description

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

Workflow position

Downstream tools

Name	output file(s)	format
TEannot	GFF with TE masked	gff

Input file

Fasta file: Genome file at fasta format

Output files

Output_name.fa: TE library
Output_name.log: log file to see each steps progress
Output_name.cfg: File to show which params have been used
Output_name.classif_stats.txt: File with statistics you can visualize
Output_name.classif: If asked, the classification file to give to next step (TEannot)

Working example

Input files

Fasta file

>dmel_chr4
GAATTCGCGTCCGCTTACCCATGTGCCTGTGGATGCCGAACAGGAGGCGCCGTTGACGGC
GAATGACTTACTCAAGGGAGTAGCCAATCTGTCGGATACGCCCGGATTGGAGCTGCCCAT
GGAGGGTTCTACAAGAAAGCGGTGGAGGATTGCTCGCATACTGCGAGACCGTTTCTGAAG
GAGATGGCTCATGGAGTACCTGCCTACGCTTGTGCGCCGCGAGAAGTGGTGAAGAAGAAC
GGAGCCCATACACCAGGGTGATATGGTCTTCGTCTGCGATCCCGCCTTGCCCCGGCGAGA
GTGGTGCAAGGGCATCATGGAGGAAGTCTCCAGCAGAGCAGATGGAGCAACGGCCTATAG
AGGACACTGATGCTACCCGTCTCTAAGCTTGCAGTTTTGGATTTAAGTGAATCGGTTATT
CACGGGGTCGGGGATGTCGCGGATCGAACGGTGCAATCGATAGGCGTAATCAGTATTTCC
AGATAGTGATAAGATTTGGTGGATAAATGTGTGCGGGCACACTAATGGCCGCCATCGTAA
GCCGCGAAAAGCTTAGCGTGCATTGTCGATCGAGAGTTTGGAGGGCAAACTGCGGTAAGA
TAAGATTAAATAATTTGTACTGAATAATCTTAAAGAATCCTGATGGAAAGCGCCATGCAG
TCACATATAATATGTGCAGAGCTCTCCTC

Output files

output fasta : TE library

>DTX-incomp_20150313101806-B-G1-Map3
ATACAGCTGCGGTTAAAATAATAGCACTACTGCAGGTGGAAAGTTGATTTCCTAAAAAAA
ATTATTAAATGTTTATATTTTTTTAAGTCAGATTGCATGAATAATAAGTACCATATGTTG
GCTCTCTGAGCAAGAAATTTTTAG
>RLX-incomp_20150313101806-B-R12-Map3_reversed
ATGATAAGTAGGCAAACTATAAAAATGTTCTATTTATGGGCTGCAATAAACATGTCACCG
GACAGCATAAGTGGCAACTACAG

output config : .cfg

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

output stats : .classif_stats.txt

LTR incomp: 1 (10.00%)
LTR total (RLX): 1 (10.00%)

ClassI + one order: 1 (10.00%)
ClassI total (RXX): 1 (10.00%)

-------------------------Summary--------------------------------

RXX: 1 (10.00%)
DXX: 9 (90.00%)
TOTAL: 10 (100.00%)

-----------------------------NOTES------------------------------

output classif : Classification file

DTX-incomp_dataset_370.dat-B-G1-Map3    542     +       ok      II      TIR     incomplete      CI=37; coding=(TE_BLRtx: TC1_DM:ClassII:TIR:Tc1-Mariner: 32.59%; TE_BLRx: Mariner-1_DAn_1p:ClassII:TIR:Tc1-Mariner: 18.43%); struct=(TElength: <700bps); other=(Other_profiles: PF13936.1_HTH_38_NA_OTHER_27.0: 77.27%(77.27%); SSRCoverage=0.03)
DTX-comp_dataset_370.dat-B-G8-Map20     1244    +       ok      II      TIR     complete        CI=50; coding=(TE_BLRtx: PROTOP:ClassII:TIR:P: 12.03%, PROTOP_A:ClassII:TIR:P: 49.14%); struct=(TElength: >1000bps; TermRepeats: termTIR: 50); other=(SSRCoverage=0.25)