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Galaxy .embl file conversion

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

galaxy .embl file repeatmasker
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updated by davidenko.bodya2013 • davidenko.bodya2013 • written by rrsowmya • rrsowmya

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

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written by rrsowmya • rrsowmya

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.

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written by Juke34 Juke34

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

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written by rrsowmya • rrsowmya

1 answer

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.

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written by Juke34 Juke34

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