Question: How to download the feature table file of whole genome
0
gravatar for iqra
8 months ago by
iqra0
iqra0 wrote:

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

snp rna-seq next-gen genome • 362 views
ADD COMMENTlink modified 8 months ago by tdmurphy160 • written 8 months ago by iqra0

feature table of what exactly? genes?

ADD REPLYlink modified 8 months ago • written 8 months ago by lieven.sterck5.8k

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.

ADD REPLYlink written 8 months ago by iqra0
0
gravatar for vkkodali
8 months ago by
vkkodali1.2k
United States
vkkodali1.2k wrote:

Check out GAG and the associated publication

ADD COMMENTlink written 8 months ago by vkkodali1.2k

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...

ADD REPLYlink written 8 months ago by iqra0
0
gravatar for tdmurphy
8 months ago by
tdmurphy160
tdmurphy160 wrote:

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.

ADD COMMENTlink written 8 months ago by tdmurphy160

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...

ADD REPLYlink written 8 months ago by iqra0
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