Which format to download ESTs for annotation with MAKER?
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21 months ago
mrmrwinter ▴ 30

Which format do i need to download ESTs in from GenBank?

Do i need the Complete Features? Or just the Sequence?

Or even just the gene information?

This is to run into MAKER so needs to be in FASTA

Many thanks.

genome annotation gene prediction • 354 views
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21 months ago
Juke34 ★ 6.4k

As you said it needs to be in Fasta format.

Here a complete programmatic solution to get all EST related to your species using conda and the GAAS toolkit.

conda create -n gaas  
conda activate gaas  
conda install gaas
gaas_ncbi_get_reference_data.pl --db nucest --organism species_name
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21 months ago

As far as I know it has to be the fasta format (== the sequences them self thus)

select "format as FASTA" from the top left and then sent to file ( upper right)

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