介绍

EDTA (The Extensive de novo TE Annotator)

工具 | EDTA: 转座子注释流程 - 图1

使用

软件下载

  1. cd /home/shwzhao/bin/SingularityDir/
  3. SINGULARITY_CACHEDIR=./
  4. export SINGULARITY_CACHEDIR
  5. singularity pull EDTA.sif docker://oushujun/edta:2.0.0
  7. singularity exec /home/shwzhao/bin/SingularityDir/EDTA.sif EDTA.pl -h
  8. ## INFO:    Converting SIF file to temporary sandbox...
  9. ## 
  10. ## ########################################################
  11. ## ##### Extensive de-novo TE Annotator (EDTA) v2.0.0  ####
  12. ## ##### Shujun Ou (shujun.ou.1@gmail.com)             ####
  13. ## ########################################################
  14. ## .......

参数说明

具体看参考吧

  • EDTA.pl

--curatedlib

--sensitive

--rmout

--exclude

--u

  • EDTA_raw.pl

--type

  • lib-test.pl

检验注释性能

运行

  1. mkdir test
  2. cd test
  4. cp /home/train/public_data/genome/Arabidopsis_thaliana/Arabidopsis_thaliana.genome.fa .
  6. singularity exec /home/shwzhao/bin/SingularityDir/EDTA.sif EDTA.pl --genome ./Arabidopsis_thaliana.genome.fa --overwrite 0 --sensitive 1 --anno 1 --threads 20
  1. genome=/pfs/proj/nobackup/fs/projnb10/hpc2nstor2024-021/shwzhao/01_research/03_assemble2/6_polish/genome.all.polished.fa
  2. EDTA.pl \
  3.   --genome ${genome} \
  4.   --overwrite 1 \
  5.   --sensitive 1 \
  6.   --anno 1 \
  7.   --threads 50 \
  8.   1> edta.out \
  9.   2> edta.err
  11. ls -lh
  12. ## total 3.2G
  13. ## -rw-rw----+ 1 shwzhao ps30521 9.4K Oct 23 10:06 edta.err
  14. ## -rw-rw----+ 1 shwzhao ps30521 2.0K Oct 23 11:43 edta.out
  15. ## lrwxrwxrwx  1 shwzhao ps30521  120 Oct 20 11:39 genome.all.polished.fa -> /pfs/proj/nobackup/fs/projnb10/hpc2nstor2024-021/shwzhao/01_research/03_assemble2/6_polish/genome.all.polished.fa
  16. ## -rw-rw----+ 1 shwzhao ps30521 752M Oct 20 11:39 genome.all.polished.fa.mod
  17. ## drwxrws---+ 2 shwzhao ps30521 4.0K Oct 23 11:43 genome.all.polished.fa.mod.EDTA.anno
  18. ## drwxrws---+ 2 shwzhao ps30521  20K Oct 21 00:38 genome.all.polished.fa.mod.EDTA.combine
  19. ## drwxrws---+ 3 shwzhao ps30521  12K Oct 23 10:06 genome.all.polished.fa.mod.EDTA.final
  20. ## -rw-rw----+ 1 shwzhao ps30521 3.9M Oct 23 10:06 genome.all.polished.fa.mod.EDTA.intact.gff3
  21. ## drwxrws---+ 5 shwzhao ps30521 4.0K Oct 21 00:23 genome.all.polished.fa.mod.EDTA.raw
  22. ## -rw-rw----+ 1 shwzhao ps30521 121M Oct 23 11:43 genome.all.polished.fa.mod.EDTA.TEanno.gff3
  23. ## -rw-rw----+ 1 shwzhao ps30521 288K Oct 23 11:43 genome.all.polished.fa.mod.EDTA.TEanno.sum
  24. ## -rw-rw----+ 1 shwzhao ps30521 8.5M Oct 23 10:03 genome.all.polished.fa.mod.EDTA.TElib.fa
  25. ## -rw-rw----+ 1 shwzhao ps30521 752M Oct 23 11:43 genome.all.polished.fa.mod.MAKER.masked
  26. ## -rw-rw----+ 1 shwzhao ps30521  440 Oct 20 11:29 run.sh

2.4 可视化

以后补充

  1. grep -v "##" Arabidopsis_thaliana.genome.fa.mod.EDTA.TEanno.gff3 | cut -f 1-5,7 | sed '1i seqid\tsource\tsequence_ontology\tstart\tend\tstrand' > ara.edta.tsv

参考

github 地址：https://github.com/oushujun/EDTA

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