Transposable Element Finder (TEF) - Detection of active transposable elements from NGS data

TEF is a high-performance detector of active transposable elements from short-reads of next generation sequencer, based on detection of Target Site Duplication (TSD) at the transposition.

News

Result of TEF is cited by a Nature communications paper
List of head and tail seqeucne pairs of transposable element in rice Update (2024-04-26)
Detection of transposed TEs in Arabidopsis thaliana herbarium specimen Update (2023-12-15)

Tutrial

Scripts and Readme: https://github.com/akiomiyao/tef/
Download the souce code from 'Code' pulldown menu or clone the code in your local machine.
```
git clone https://github.com/akiomiyao/tef.git
```
'tef' directory will be cleated. All codes will be saved into the tef directory.
Download fastq files
The following explanation uses nucleotide sequence data obtained from two individuals of Drosophila melanogaster, which are relatively small in size and require short analysis time.
Download from DDBJ DRA page,
https://ddbj.nig.ac.jp/resource/sra-run/SRR823377
SRR823377_1.fastq.bz2 and SRR823377_2.fastq.bz2
https://ddbj.nig.ac.jp/resource/sra-run/SRR823382
SRR823382_1.fastq.bz2 and SRR823382_2.fastq.bz2
Files with bz2 format can also be analyzed by tef.pl.

Or download fastq.gz files from NCBI using fastq-dump.
'fastq-dump' can be installed by apt command (Ubuntu).
e.g. apt install fastq-dump
fastq-dump --split-files SRR823377 SRR823382

First run of tef.pl


git clone https://github.com/akiomiyao/tef.git
cd tef
mkdir SRR823377 SRR823382
mkdir SRR823377/read
mkdir SRR823382/read
mv Download/SRR823377.fastq.gz SRR823377/read
mv Download/SRR823382.fastq.gz SRR823382/read
mkdir dmel
cd dmel
curl -O ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.26_FB2019_01/fasta/dmel-all-chromosome-r6.26.fasta.gz
cd ..
perl tef.pl a=SRR823377,b=SRR823382,ref=dmel

Options are separated by comma. Do not add space after comma.

At the first run of tef.pl. 'config' file is created in the reference directory.
Edit config file in tef/dmel directory. Scaffold may be not required.
If names of scaffold are changed to 'NOP', nucleotide seqeunce of scaffold will be ignored.
For example,
```
2L
2R
3L
3R
4
X
Y
NOP
NOP
NOP
NOP
NOP
NOP
continue to line number 1870.
```
If you feel hard to change to NOP, open config file by Excel, and paste 'NOP' in all scaffold cells, and save 'config' in the 'tef/dmel' directory as a text file.
Link to 'config' file for Drosophila melanogaster.
Run again tef.pl
```
perl tef.pl a=SRR823377,b=SRR823382,ref=dmel
```
Default is mode of 'Junction method'.
For the analysis 'TSD method', specify the value of 'tsd_size'.
For example,
```
perl tef.pl a=SRR823377,b=SRR823382,ref=dmel,tsd_size=8
```

Results are saved in the 'SRR823377' (specified with 'a') directory.

child/
count.20/
count.8/
junction_method.genotype.SRR823377.SRR823382
junction_method.log
junction_method.summary.SRR823377.SRR823382
junction_method.tepos.SRR823377.SRR823382
junction_method.verify.SRR823377.SRR823382
read/
split/
tmp/
tsd_method.genotype.SRR823377.SRR823382.8
tsd_method.log.8
tsd_method.pair.SRR823377.SRR823382.8
tsd_method.summary.SRR823377.SRR823382.8
tsd_method.tepos.SRR823377.SRR823382.8
tsd_method.verify.SRR823377.SRR823382.8

Following is a part of genotype file of TSD method.

                                                                                                                                                                   SRR823377              SRR823382             
Accession   Chr.  Head Junction  Tail Junction  Direction TE Head                 TE Tail                 Head Flanking          TSD        Tail Flanking          Head   Tail  No-ins.   Head    Tail   No-Ins.  Genotype
SRR823377   3L    11009306       11009313       r         CATGATGAAATAACATAAGG    CCTTATGTTATTTCATCATG    CGGCGAATGAGAGGCCAACA   GGCCAACA   GGCCAACAGTCGGCACTAAC   5      7     15        0       0      26       H
SRR823377   3L    11009313       11009306       f         CATGATGAAATAACATAAGG    CCTTATGTTATTTCATCATG    GTTAGTGCCGACTGTTGGCC   TGTTGGCC   TGTTGGCCTCTCATTCGCCG   7      5     17        0       0      23       H
SRR823377   3L    13569996       13570003       r         CAGAGAACTGCAAGGGTGGC    TGGCGGGCTGCAGTTCTCTG    ATGGTGGTGTGCATGTGGGG   ATGTGGGG   ATGTGGGGTAACCTGCCCAA   25     15    0         0       0      16       M
SRR823377   3L    13570003       13569996       f         CAGAGAACTGCAGCCCGCCA    GCCACCCTTGCAGTTCTCTG    TTGGGCAGGTTACCCCACAT   CCCCACAT   CCCCACATGCACACCACCAT   15     25    0         0       0      13       M
SRR823377   3L    16020833       16020840       r         CAGAGAACTGCAAGGGTGGC    TGGCGGGCTGCAGTTCTCTG    CAACAGATGGGCTCCCGGAT   TCCCGGAT   TCCCGGATCGCCGGTCGCCG   19     10    0         0       0      27       M
SRR823377   3L    16020840       16020833       f         CAGAGAACTGCAGCCCGCCA    GCCACCCTTGCAGTTCTCTG    CGGCGACCGGCGATCCGGGA   ATCCGGGA   ATCCGGGAGCCCATCTGTTG   10     19    0         0       0      27       M
SRR823377   3L    23672618       23672625       r         CATGATGAAATAACATAAGG    CCTTATGTTATTTCATCATG    CCGCTGCGCTTGGGATAGCC   GGATAGCC   GGATAGCCTAACTAATTAGA   9      7     395       0       0      315      H
SRR823377   3L    23672619       23672626       r         CCATGATGAAATAACATAAG    ACCTTATGTTATTTCATCAT    TCCGCTGCGCTTGGGATAGC   GGGATAGC   GGGATAGCCTAACTAATTAG   9      7     397       0       0      325      H
SRR823377   3L    23672625       23672618       f         CATGATGAAATAACATAAGG    CCTTATGTTATTTCATCATG    TCTAATTAGTTAGGCTATCC   GGCTATCC   GGCTATCCCAAGCGCAGCGG   7      9     64        0       0      71       H
SRR823377   3L    23672626       23672619       f         ATGATGAAATAACATAAGGT    CTTATGTTATTTCATCATGG    CTAATTAGTTAGGCTATCCC   GCTATCCC   GCTATCCCAAGCGCAGCGGA   7      9     63        0       0      71       H

The result file is tab separated text file, and can be opened by Excel.
The CATGATGAAATAACATAAGG-CCTTATGTTATTTCATCATG head-tail pair is P-element.
Numbers of Head, Tail, and No-ins. are read counts containing junction of head, junction of tail, and No-insertion (wild-type) from SRR823377 and SRR823382.
Forward and complementary seqeunces of TE Head and TE Tail are listed.
If counts of Head, Tail and No-ins. are detected in SRR823377 and only counts of No-Ins. are detected in SRR823382, TE is transposed into only SRR823377 and genotype is Heterozygous (shown in 'H').
If counts of Head, Tail are detected and no count for No-ins. in SRR823377 and only counts of No-Ins. are detected in SRR823382, TE is transposed into only SRR823377 and genotype is Homozygous (shown in 'M').
The high counts of No-insertion indicats that the transposed region is in the repetitive region.
If pair of adjuscent bases of TSD is complementary, tef.pl detects both positions as junctions. e.g., 3L 23672618 and 23672619.

Citing TEF

Miyao, A., Yamanouchi, U. Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. BMC Bioinformatics 23, 500 (2022). https://doi.org/10.1186/s12859-022-05011-3

Contact

Akio Miyao, Ph.D (miyao@affrc.go.jp)