Question: Adding CDS features to Gff3 file
0
gravatar for abhijit.synl
17 months ago by
abhijit.synl50
United States
abhijit.synl50 wrote:

Hello,

I would like to add the CDS feature to my Gff3 file, that has exons in it. I saw that genometools can do this for you

gt cds -startcodon -finalstopcodon -seqfile foo.fasta -o foo.gff3 [GFF3-FILE]

I am looking for the CDS to be the longest ORF with an ATG start codon per mRNA. Will the above command give me that? Secondly I did not see a flag for specifying the genetic code. Is this by default "standard vertebrate"?

Thanks for the help Abhijit

ADD COMMENTlink modified 22 days ago • written 17 months ago by abhijit.synl50

This is resolved. please close thread

ADD REPLYlink written 22 days ago by abhijit.synl50
0
gravatar for abhijit.synl
22 days ago by
abhijit.synl50
United States
abhijit.synl50 wrote:

Though not directly but can be acheived using a combination of Genometools and PASA

ADD COMMENTlink written 22 days ago by abhijit.synl50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 794 users visited in the last hour