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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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*.pass.list and *.pass.list.gff3 have different row number #39

Closed SCQUchenyang closed 5 years ago

SCQUchenyang commented 5 years ago

Hi， I have run LTR_retriever with the output from LTR-finder and LTRharvest. I have got the result.But I find the .pass.list.gff3 have 38264 rows，but .pass.list only has 5236 rows. I want to get insert time of all intact LTR-RTs. The *.pass.list only show some of them? And, I have another question.Can LTR_retriever class the LTR-RT(Copia and Gyspy) into smaller family?such as TAT or Tork？ Thanks for your time and help. Chenyang

oushujun commented 5 years ago

Hello Chenyang,

Thanks for using LTR_retriever. Your numbers make sense to me. If you take a closer look at the .pass.list.gff3 file, you may find each intact LTR element is described by 7 lines. If you are looking for insertion times of each intact element, you may use the .pass.list file, in which the last column is the estimated insertion time based on the JC69 model.

The current version of LTR_retriever only classifies intact elements into Copia/Gypsy. For further classification, you may want to use HMMER and related HMM profiles.

Please let me know if you have further questions.

Thanks, Shujun