Question: Adding Gene Name attribute to CDS feature ??
0
gravatar for Mostafa Mahmoud
7 weeks ago by
china
Mostafa Mahmoud0 wrote:

how i can add Gene name (Name=value in Gene Feature ) att to CDS and exon feature??

  chr1  transdecoder    gene    11013482    11051446    .   -   .   ID=CSG00000000267;Name=TWiK family of potassium channels protein 7-like isoform X1|1.20E-222|
chr1    transdecoder    mRNA    11013482    11051446    .   -   .   ID=CSM00000000267;Parent=CSG00000000267;Name=TWiK family of potassium channels protein 7-like isoform X1|1.20E-222|
chr1    transdecoder    exon    11013482    11015247    .   -   .   ID=CSE00000000985;Parent=CSM00000000267
chr1    transdecoder    exon    11028188    11028396    .   -   .   ID=CSE00000000986;Parent=CSM00000000267
chr1    transdecoder    exon    11029544    11029744    .   -   .   ID=CSE00000000987;Parent=CSM00000000267
chr1    transdecoder    exon    11032351    11032509    .   -   .   ID=CSE00000000988;Parent=CSM00000000267
chr1    transdecoder    exon    11032781    11032904    .   -   .   ID=CSE00000000989;Parent=CSM00000000267
chr1    transdecoder    exon    11034062    11034235    .   -   .   ID=CSE00000000990;Parent=CSM00000000267
chr1    transdecoder    exon    11042353    11042709    .   -   .   ID=CSE00000000991;Parent=CSM00000000267
chr1    transdecoder    exon    11051353    11051446    .   -   .   ID=CSE00000000992;Parent=CSM00000000267
chr1    transdecoder    CDS 11015089    11015247    .   -   0   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11028188    11028396    .   -   2   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11029544    11029744    .   -   2   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11032351    11032509    .   -   2   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11032781    11032904    .   -   0   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11034062    11034235    .   -   0   ID=CSC00000000267;Parent=CSM00000000267
chr1    transdecoder    CDS 11042353    11042505    .   -   0   ID=CSC00000000267;Parent=CSM00000000267
gff annotation genome • 162 views
ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Mostafa Mahmoud0

Hello Mostafa. What is your species of study?

ADD REPLYlink written 7 weeks ago by Kevin Blighe61k

Chilo supperssalis denovo species

ADD REPLYlink written 7 weeks ago by Mostafa Mahmoud0

Interesting... the Asiatic rice borer. I will get back to this in the morning (or somebody else may help).

ADD REPLYlink written 7 weeks ago by Kevin Blighe61k

i have skills in annotation of non model organism but some times i stuck in simple stuff because my background is biology not computer science

ADD REPLYlink written 7 weeks ago by Mostafa Mahmoud0

Are you sure the species is correct? - according to Ensembl, the identifiers should begin with 'csug'

See here: http://ensembl.lepbase.org/Chilo_suppressalis_csuogs1/Info/Index

How did you produce your output file? Can you show all commands?

ADD REPLYlink written 7 weeks ago by Kevin Blighe61k

this my own id i am working on new version

ADD REPLYlink written 7 weeks ago by Mostafa Mahmoud0

Okay, but, I am not sure that I can help, in that case. If there is no previous information for your own IDs that you have created, then I am not sure what I (or anybody else) can do.

Or, you could try to overlap the co-ordinates of your new genes to those already identified. There are GFF files available through the link that I showed.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Kevin Blighe61k

i just want cp the available in the gff annotation to cds and exon feature

ADD REPLYlink written 7 weeks ago by Mostafa Mahmoud0
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