Transform repeatmasker output into gff

Question

[SeaStar]

Hello! I used repeatmasker to find transposable elements in my genome. Repeatmasker produced some outputs. I have myfile.fa.out and I need to transform it into gff. There is a code or program to transform it into gff? Thank you.

Answer 1

[AK]

some outputs

What did you get exactly? When running RepeatMasker, by adding -gff it will give you a gff output.

However, you can still do:

1. Use RMout_to_bed.pl to parse *.out from RepeatMasker
2. Then convert the bed to gff

[SeaStar]

I've also produced a bed file, but I don't know how to transform it to gff. Other outputs are a .cat file, and a .tbl. anyway I can run again repeatmasker -gff with my .fa.out file to obtain the gff?

[AK]

I've also produced a bed file, but I don't know how to transform it to gff

Try genometools: gt bed_to_gff3 or BED-to-GFF in Galaxy.

I can run again repeatmasker -gff with my .fa.out file to obtain the gff?

No, with the original unmasked .fa (re-do masking).

[SeaStar]

Thank you very much :)