repbase and flybase

[Rui Guo]

I want to make a gff file about the TE in fly, so I can see the repeat position in IGV. I can use repeatmasker, based on the repeat data from repbase file drorep.ref, which contains 238 sequences. I also see there are two precomputed files in flybase website

ftp://flybase.net/genomes/Drosophila...r6.10.fasta.gz
ftp://flybase.net/genomes/Drosophila...r6.10.fasta.gz


I don't know what's the relation between those files. Are the result from repeatmasker less reliable than the fasta files above? Which file should I use if I use the precomputed files?

[GenoMax]

If you want pre-computed repeatmasker files for fly genome they are available in this directory: http://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/

[Rui Guo]

Thank you. Can I use the flybase files? Is there a big difference between the flybase files and repeatmasker result? Also what's the difference between the flybase interspersed repeat file and transposon repeat files?