Script convert ltr_finder output file to fasta format

Question

[Ginsea Chen]

Dear all

Now I want to extract fasta file from LTR-finder output , while I have poor program knowledge, and don't know how to do it. So I want to ask if anyone can provide me an available script or method to do this. Thanks!

[TWV]

Have you found a solution? if so, please share. Same question here.

Answer 1

[TWV]

First use cnv_ltrfinder2gff.pl to convert the output to gff format, then use bedtools getfasta to convert gff to a fasta list.