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