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How To Make The 9Th Column Of A Gff3 File??

How to fill make the 9th column for the gff3 file??

AB00001 interproscan    gene    1       1945    .       -       .       ID=TC00001.1;Parent=AB00001.1;
AB00001 interproscan    mRNA    1       1945    .       -       .       ID=AB00001.1.mRNA;Parent=AB00001.1;
AB00001 interproscan    five_prime_UTR  1797    1945    .       -       .       ID=AB00001.1.five_prime_UTR;Parent=AB00001.1;
AB00001 interproscan    CDS     528     1796    .       -       0       ID=AB00001.1.CDS;Parent=AB00001.1;
AB00001 interproscan    three_prime_UTR 1       527     .       -       .       ID=AB00001.1.three_prime_UTR;Parent=AB00001.1;
gff3 ngs annotation
• 2,721 views • link
updated by Ram Ram • written by alok.helix alok.helix

I guess it depends on what you want to make it from. If there are no IDs/gene names for the species you're working on then you have a good bit of freedom in what everything gets called.

• 117 views • link
written by Devon Ryan Devon Ryan

This is usually filled by data sources or custom made programs. If you want to add fields based on some other data that you have just post the type of data and we could perhaps tell you what to do.

Either way the question needs more specificity as to what you would want in that column.

• 192 views • link
written by Istvan Albert Istvan Albert

I just want to fill that column so that it can be accepted by snpEFF for further anntation. I used the online validator on SO webpage but it fails it everytime despite of me doing whats required...I have two gff files one from transdecoder and other from interproscan, but the IPR file is not the valid in snpEFF thus am modifying then existing IPR file

• 0 views • link
written by alok.helix alok.helix

ok so your question is really about what type of fields are required for snpEff to work. That is very different from what you are asking right now.

• 239 views • link
written by Istvan Albert Istvan Albert

bro...the output of transdecoder and interproscan do not match thus i decided to make a gff3 file similar to that of transdecoder. Now that i have made nearly all the field similar to transdecoder's output, i donot know what info should i incorporate in my 9th column,I can leave it as a ".(dot)" but for some cryptic reason snpeff is not updating it's database for this gff3 file.Technically its should.....Thank you for the interaction

• 0 views • link
written by alok.helix alok.helix

Hello alok.helix!

We believe that this post is unanswerable as is, so we are closing it.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. We would be happy to reopen if you provide some clarification.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 2 views • link
written by Daniel Standage Daniel Standage

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