Convert Gff To Gtf

Question

[upendrakumar.devisetty]

I don't know what is wrong with my GFF file. I couldn't been able to convert to GTF. Any help would be appreciated

##gff-version 3
A04     blast   match   3897075 3897167 35.8    +       .       ID=BR_14_G1;Target=BR_14;align=93
A04     blast   HSP     3897075 3897167 35.8    +       .       Parent=BR_14_G1;Target=BR_14 277 555;align=93
A10     blast   match   991755  991829  50      +       .       ID=BR_14_G2;Target=BR_14;align=75
A10     blast   HSP     991755  991794  26.9    +       .       Parent=BR_14_G2;Target=BR_14 2768 2896;align=43
A10     blast   HSP     991798  991829  23.1    +       .       Parent=BR_14_G2;Target=BR_14 2986 3081;align=32
A08     blast   match   14081778        14081874        48.1    +       .       ID=BR_14_G3;Target=BR_14;align=72
A08     blast   HSP     14081778        14081820        25.0    +       .       Parent=BR_14_G3;Target=BR_14 2768 2896;align=43
A08     blast   HSP     14081846        14081874        23.1    +       .       Parent=BR_14_G3;Target=BR_14 2986 3072;align=29

[Sukhi Singh]

Whats the error and what tool are you using for the conversion

Answer 1

[Malachi Griffith]

GFF is the same as GTF except for the 9th column.

GTF (Gene Transfer Format) is a refinement to GFF that tightens the specification. The first eight GTF fields are the same as GFF. The group field has been expanded into a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space

There may be other problems with your file but it appears that your type/value pairs are separated by '=' instead of exactly one space. You could try to match your output to the examples here:

http://genome.ucsc.edu/FAQ/FAQformat.html#format4

http://mblab.wustl.edu/GTF2.html

AB000381 Twinscan  CDS          380   401   .   +   0  gene_id "001"; transcript_id "001.1";
AB000381 Twinscan  CDS          501   650   .   +   2  gene_id "001"; transcript_id "001.1";
AB000381 Twinscan  CDS          700   707   .   +   2  gene_id "001"; transcript_id "001.1";
AB000381 Twinscan  start_codon  380   382   .   +   0  gene_id "001"; transcript_id "001.1";
AB000381 Twinscan  stop_codon   708   710   .   +   0  gene_id "001"; transcript_id "001.1";

[Istvan Albert]

just an observation the original poster has a GFF3 file whereas the GTF is a refinement over the GFF2 specification. In the GFF3 format the key/values are separated by = sign.

[Malachi Griffith]

Ah, good point...