Question: Galaxy .embl file conversion
0
gravatar for rrsowmya
28 days ago by
rrsowmya20
United States
rrsowmya20 wrote:

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

ADD COMMENTlink modified 27 days ago • written 28 days ago by rrsowmya20

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

ADD REPLYlink written 28 days ago by genomax92k

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

ADD REPLYlink written 27 days ago by rrsowmya20

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.

ADD REPLYlink written 27 days ago by Juke344.9k

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

ADD REPLYlink written 26 days ago by rrsowmya20
1
gravatar for Juke34
28 days ago by
Juke344.9k
Sweden
Juke344.9k wrote:

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.

ADD COMMENTlink written 28 days ago by Juke344.9k
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