search

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
MIT License
188 stars 32 forks source link

Extract transposon #71

Open Wenwen012345 opened 2 years ago

Wenwen012345 commented 2 years ago

Hello author I used the LTR-retriever to extract the transposon of a species, assuming a GFF file named 1.fna.mod.ltr.gff3 was generated. Assume that the genome GFF file of the species is GCA_009746105.1_ASM974610v1_genomic. 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 "). Error: cannot locate input file: ## GFF -version 3

Here is the GFF file format for input: CM019264.1 LTR_retriever Gypsy_LTR_retrotransposon 1 327 1604 - . ID=LTR_homo_0;Name=CM019264.1:9232801..9243066_INT;Classification=LTR/Gypsy;Sequence_ontology=SO:0002265;Identity=0.804;Method=homology CM019264.1 LTR_retriever Gypsy_LTR_retrotransposon 2761 3035 947 - . ID=LTR_homo_1;Name=QEFC01004019.1:152484..162804_INT;Classification=LTR/Gypsy;Sequence_ontology=SO:0002265;Identity=0.769;Method=homology

Wenwen012345 commented 2 years ago

The article links: https://onlinelibrary.wiley.com/doi/10.1111/jse.12850