Question: How to download the feature table file of whole genome
0
gravatar for iqra
7 days 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 • 126 views
ADD COMMENTlink modified 5 days ago by tdmurphy160 • written 7 days ago by iqra0

feature table of what exactly? genes?

ADD REPLYlink modified 7 days ago • written 7 days ago by lieven.sterck3.5k

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 6 days ago by iqra0
0
gravatar for vkkodali
6 days ago by
vkkodali860
United States
vkkodali860 wrote:

Check out GAG and the associated publication

ADD COMMENTlink written 6 days ago by vkkodali860

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 1 day ago by iqra0
0
gravatar for tdmurphy
5 days 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 5 days 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 1 day ago by iqra0
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