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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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"?" strand direction in 'gff3' #69

Closed Dobkin-Sun closed 4 years ago

Dobkin-Sun commented 4 years ago

Dear Shujun, After using v2.8.6,I found a problem about the gff3 file. First, the first eight annotations of gff3 don't have 'seqid' information. And the ninth annotion has a 'Boutg12958pilon' seqid which doesn't exist in source fasta file. The beginning of 'Boutg' looks like that the annotation of intact LTR went wrong. Second, lots of annotations don't have correct strand direction of "+" or "-" and there are a lot of directions of "?" in file. Best Sun Daojin

oushujun commented 4 years ago

Hi Daojin,

Your source file may have complex sequence names and the program automatically shorten the name for you. You may want to do it yourself to make the downstream easier. This thread can answer your second question: https://github.com/oushujun/EDTA/issues/80

Best, Shujun

Dobkin-Sun commented 4 years ago

Thank you again, Dr Ou.