Bypass dfam

Open tzvi909 opened this issue 1 year ago • 1 comments

What do you want to know?

Would it be possible to bypass the dfam db and basically just run repeatmasker with an RMBlast search, for example, against a lib fasta made from your species of choice from the dfam db with the native famdb.py script to avoid having to use a ~70GB file.

Have you installed RepBase RepeatMasker Edition for RepeatMasker? No.

Jun 03 '24 13:06 tzvi909

The next release of RepeatMasker ( preparing the release now ), will not require downloading Dfam in order to perform custom library searches ( "-lib" ).

Aug 08 '24 19:08 rmhubley

RepeatMasker 4.1.7 was just release and fixes this issue. You should be able to run custom library searches (-lib) out of the box without having to download/store Dfam.

Sep 11 '24 20:09 rmhubley