Question: Relate CDS annotation to parent gene
gravatar for Mostafa Mahmoud
4 months ago by
Mostafa Mahmoud0 wrote:

i made gff annotation file with cds functional annotation i want add parent id to all transcript annotation including exon utr cds mrna and relate all of them to parent gene and change gene name by cds name


sample file

gff genome • 164 views
ADD COMMENTlink modified 3 months ago by Juke-343.3k • written 4 months ago by Mostafa Mahmoud0
gravatar for Juke-34
3 months ago by
Juke-343.3k wrote:

I think you are screw because you don't have ID/Parent attributes to link the related-features together, neither a shared attribute between the related-features (i.e locus_tag), and it cannot be parsed sequentially because the file has been sorted and features related to a same record are spread over the file.

You can maybe try to use the ID of features as a shared attribute by clipping the suffix (prefix are similar between the CDS,mRNA, gene ...)

ADD COMMENTlink written 3 months ago by Juke-343.3k
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