search

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
188 stars 40 forks source link

Can you send me find_ltr_DAWGPAWS.pl you have used? #35

Closed wangzhennan14 closed 5 years ago

wangzhennan14 commented 5 years ago

Hi, Can you send me the MGEScan_LTR packages you have used in this paper? I have downloaded some packages, but they did not work. Could you send me the (a modified version obtained from DAWGPAWS) to wangzhennan@ioz.ac.cn? Thank you very much!

                                                                      Wangzhennan
oushujun commented 5 years ago

Dear Wangzhennan,

You may download MGEScan_LTR and the PAWGPAWS version from here: http://darwin.informatics.indiana.edu/evolution/data/sw/

Previously, I just modified file paths to dependent programs in find_ltr_DAWGPAWS.pl. However, the search engine of this package is too old to run in my new HPC environment, and I could not make it run anymore. You may want to try it yourself: cd ./ltr/MER ./ltr If it gives you help info, then it still works in your system. Then you may want to read the README and modify dependencies in find_ltr_DAWGPAWS.pl. What you want to get from this program is the output format like LTRharvest, which require some coding skills to transform the original output, then feed the output to LTR_retriever by: ./LTR_retriever -inharvest MGEScan_LTR.output

I will close this thread for now. You may reopen it or comment below if you have further questions.

Good luck!

Best, Shujun