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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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GFFCompare #120

Closed Wenwen012345 closed 2 years ago

Wenwen012345 commented 2 years ago

Hello @oushujun I used the LTR-retriever to extract the transposon of a species, assuming a GFF file named 1.fna.mod.ltr.homo.gff3 was generated. Assume that the genome GFF file of the species is GCA_009746105.1_ASM974610v1_genomic.gff. How to correctly extract transposon insertion sites by GFFCompare (see article "Characterization of Genome-Wide Long Terminal Repeat Retrotransposons provide insights into trait evolution of four grapevine species ",https://onlinelibrary.wiley.com/doi/10.1111/jse.12850).

When I use it, I get the following prompt:

manager@bl8vbox[gff] gffcompare -r ./GCA_009746105.1_ASM974610v1_genomic.gff -T -V -o 1 -s ../1.fna -p 1 ./1.fna.mod.LTR.homo.gff3 Prefix for output files: 1 Loading reference transcripts.. 23559 reference transcripts loaded. Loading query file #1: ./1.fna.mod.LTR.homo.gff3 0 query transfrags loaded. Cleaning up.. Done.

The result file is empty.

oushujun commented 2 years ago

Hello,

This seems like an issue of GFFCompare. Please seek their help. Thanks!

Shujun

Wenwen012345 commented 2 years ago

Sorry to have taken up your time