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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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Questions about *.pass.list #29

Closed rapaJiahe closed 5 years ago

rapaJiahe commented 5 years ago

Hi Shujun,

From the log file, i know *.pass.list contain the whole genome LTR-RTs (redundant). I found some LTR-RT have the same coordinate with different TSD. C01:2584769..2588663 pass motif:TGCA TSD:ATTAC 2584764..2584768 2588664..2588668 IN:2585668..2587763 0.9911 ? unknown NA 344355 C01:2584769..2588663 pass motif:TGCA TSD:GTAAT 2584764..2584768 2588664..2588668 IN:2585668..2587763 0.9911 - unknown NA 344355

I don't know why this happens. Are both results reliable LTR-RTs?

Best, Jiahe

oushujun commented 5 years ago

28

oushujun commented 5 years ago

Hi Jiahe,

This is the same element which is likely a genuine LTR element. One of the TSDs was not converted to the complementary form due to the ambiguity of direction. I have fixed this minor bug in the later updated version. Thanks for using LTR_retriever!

Cheers, Shujun