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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Support for MGEScan #19

Closed zengxiaofei closed 6 years ago

zengxiaofei commented 6 years ago

Hi Dr. Ou,

According to the manual of LTR_retriever, the input from MGEScan was generated by "a modified version of DAWGPAWS" -- find_ltr_DAWGPAWS.pl. And bin/run_MGEScan.pl also calls for the script:

my $DAWGPAWS_path="/mnt/home/oushujun/git_bin/MGEScan_LTR";

However, it seems that the script has not been provided in the LTR_retriever.

I have tried to use the original version of DAWGPAWS by myself, but it is quite hard to use. I should be most grateful if you would send me the script (Email: xiaofei_zeng@whu.edu.cn).

Thank you very much Xiaofei

oushujun commented 6 years ago

Dear Xiaofei,

Thank you for using LTR_retriever. The MGEScan_LTR was used in our paper for the purpose of benchmarking. As you experienced, it requires some modifications for further use. I didn't provide the modified code because it's not necessary to use MGEScan_LTR as I mentioned in #8 and in our paper. The inclusion of MGEScan_LTR only improve the sensitivity marginally and will also introduce false discovery. Thus it's not worth the trouble.

If you want to use it anyways, you can try to modify the output of MGEScan_LTR into the LTRharvest format, then feed the program by -inharvest converted.scn.

Thanks!

Shujun

zengxiaofei commented 6 years ago

Thank you very much!