How to download the feature table file of whole genome

Question

[iqra]

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

[lieven.sterck]

feature table of what exactly? genes?

[iqra]

tbl file (feature table file, http://www.ncbi.nlm.nih.gov/projects/Sequin/table.html)enter link description here. It can be downloaded from NCBI directly.

Answer 1

[vkkodali_ncbi]

Check out GAG and the associated publication

[iqra]

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...

Answer 2

[tdmurphy]

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.

[iqra]

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...