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CSU-KangHu / HiTE

High-precision TE Annotator
GNU General Public License v3.0
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Classification and insertion time of transposons #7

Closed MrbrilliantLL closed 1 month ago

MrbrilliantLL commented 1 month ago

Hello, I have two questions about the HiTE output files:

First, it seems that the naming of transposon classification in the HiTE.tbl and HiTE.out files is inconsistent. Where can I find the correspondence between the two classification methods?

Second, the HiTE parameters can be set with --miu, but I did not find statistical information about transposon insertion time in the output files.

Looking forward to your response.

CSU-KangHu commented 1 month ago

Hi @MrbrilliantLL,

First, it seems that the naming of transposon classification in the HiTE.tbl and HiTE.out files is inconsistent. Where can I find the correspondence between the two classification methods?

I assume you want to obtain a more detailed genomic proportion for each type of TE. You can follow these steps:

  1. Modify the Taxonomy.pm file in RepeatMasker. For example, my path is /home/hukang/miniconda3/envs/HiTE/share/RepeatMasker/Taxonomy.pm. Comment out line 72 (use Text::Soundex;) using #.
  2. Run buildSummary.pl using the absolute path. For example, my command is /home/hukang/miniconda3/envs/HiTE/share/RepeatMasker/util/buildSummary.pl HiTE.out > HiTE.detail.tbl.
  3. You will get detailed annotation information, including the annotation proportion for each transposon. Detailed Annotation

Second, the HiTE parameters can be set with --miu, but I did not find statistical information about transposon insertion time in the output files.

HiTE currently utilizes LTR_retriever to identify LTR transposons. Therefore, the --miu parameter is actually passed to LTR_retriever. You can check the genome.rename.fa.pass.list file to find the insertion times corresponding to LTRs.

Best, Kang

MrbrilliantLL commented 1 month ago

Thank you again for your prompt response. Your answer has effectively solved my problem. I will close this issue.