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How to download the feature table file of whole genome

How to download the feature table file of wheat whole genome which is used in RNA Editing Detection in Organelle (REDO) TOOL ... enter link description here

rna-seq genome next-gen snp
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updated by tdmurphy tdmurphy • written by iqra • iqra

feature table of what exactly? genes?

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written by lieven.sterck lieven.sterck

2 answers

Check out GAG and the associated publication

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written by vkkodali_ncbi vkkodali_ncbi

I used the GAG .by runing this command python gag.py -f Triticum_aestivum.fa --gff Triticumgff3.gff3 --out gag_output

but the gag_output folder is empty...

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written by iqra • iqra

REDO sounds like it is specific for organelles -- is it valid to run on a whole genome?

There are some annotated organelle sequences available for wheat, including two in RefSeq: https://www.ncbi.nlm.nih.gov/nuccore/?term=txid4565%5BOrganism%3Aexp%5D+AND+complete+genome%5Btitle%5D You can get feature table output for those from the "Send to" option. Check off the sequences of interest, and under "Send To" select "File" and "Feature Table"

For the whole genome, it looks like the IWGSC wheat genome in GenBank doesn't have any annotation, and it hasn't been annotated by NCBI in RefSeq: https://www.ncbi.nlm.nih.gov/assembly/GCA_900519105.1 So you can't download feature table format from NCBI.

GAG on the GFF3 available from IWGSC might work.

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written by tdmurphy tdmurphy

I used the GAG .by runing this command python gag.py -f Triticum_aestivum.fa --gff Triticumgff3.gff3 --out gag_output

but the gag_output folder is empty...

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written by iqra • iqra

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