Galaxy .embl file conversion

Question

[rrsowmya]

Hi,

I am trying to use Maker in in Galaxy. To perform repeat masking, I have a .embl file of known repeats but which format/ file type do I load it in? I have tried loading the file as GFF3. GTF, FASTA but all says file unavailable.

Thanks in advance, Sowmya

[GenoMax]

Please post this over at Galaxy help forum to get specific help with Galaxy: https://help.galaxyproject.org/

[rrsowmya]

Thank you! I will try, however, MAKER doesn't accept FASTA files in the repbase input column.

[Juke34]

I don't know how it works on Galaxy, my answer suits a use of MAKER as a standalone program. So as suggested by @genomax, you better to ask on the Galaxy forum.

[rrsowmya]

Thanks Juke34 and genomax. I still haven’t found a solution but I will post on galaxy help.

Answer 1

[Juke34]

You need to use buildRMLibFromEMBL.pl from RepeatMasker to convert the EMBL file into fasta. Then it is the Fasta file then you have to provide to MAKER.