gff > gtf transformation problem

Minseok Seo

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Join Date: Oct 2014

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gff > gtf transformation problem

10-19-2014, 05:09 PM

I want to generate gtf file for RNA-seq analyse...

But, I experienced my first for performing RNA-seq analysis without gtf file.

Input data are as following :

Chr0 GLEAN mRNA 13595835 13596290 0.919626 + . ID=Cla000001;
Chr0 GLEAN CDS 13595835 13596290 . + 0 Parent=Cla000001;
Chr0 GLEAN mRNA 22577757 22577987 0.831796 + . ID=Cla000002;
Chr0 GLEAN CDS 22577757 22577987 . + 0 Parent=Cla000002;
Chr0 GLEAN mRNA 258813 259526 0.919626 + . ID=Cla000003;
Chr0 GLEAN CDS 258813 259526 . + 0 Parent=Cla000003;
Chr0 GLEAN mRNA 301272 301643 0.867498 - . ID=Cla000004;
Chr0 GLEAN CDS 301272 301643 . - 0 Parent=Cla000004;
Chr0 GLEAN mRNA 319902 320398 1 - . ID=Cla000005;
Chr0 GLEAN CDS 320342 320398 . - 0 Parent=Cla000005;
Chr0 GLEAN CDS 319902 320039 . - 0 Parent=Cla000005;
Chr0 GLEAN mRNA 6029352 6029806 1 + . ID=Cla000006;
Chr0 GLEAN CDS 6029352 6029441 . + 0 Parent=Cla000006;
Chr0 GLEAN CDS 6029549 6029806 . + 0 Parent=Cla000006;
Chr0 GLEAN mRNA 393272 393487 0.999939 + . ID=Cla000007;
Chr0 GLEAN CDS 393272 393487 . + 0 Parent=Cla000007;
Chr0 GLEAN mRNA 432273 433147 0.932871 - . ID=Cla000008;
Chr0 GLEAN CDS 432835 433147 . - 0 Parent=Cla000008;
Chr0 GLEAN CDS 432273 432742 . - 2 Parent=Cla000008;
Chr0 GLEAN mRNA 441325 441645 0.999939 + . ID=Cla000009;
Chr0 GLEAN CDS 441325 441645 . + 0 Parent=Cla000009;
Chr0 GLEAN mRNA 9242106 9242594 1 + . ID=Cla000010;
Chr0 GLEAN CDS 9242106 9242160 . + 0 Parent=Cla000010;
Chr0 GLEAN CDS 9242413 9242594 . + 2 Parent=Cla000010;

Third column have only CDS or mRNA because it may plant...

As we can see ftp://www.icugi.org/pub/genome/water...elon_v1.gff.gz, more detailed information can be obtained...

As a result, I want to know that how to generate gtf file using such gff file.

(code, methods, anything OK)
Thanks.~
Tags: gtf gff

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