Question: Repeat masked GFF3 not being converted to GTF
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gravatar for james.lloyd
18 months ago by
james.lloyd80
United States
james.lloyd80 wrote:

I am trying to convert the GFF3 file of the version 3.3 of the moss (Physcomitrella patens) genome into a GTF file with: gffread my.gff3 -T -o my.gtf This worked fine when I was converting the gene GFF3 to GTF (Ppatens_318_v3.3.gene_exons.gff3). The error I am getting with the repeatmasked version is an empty GTF file (with no error messages). Below is the first 10 lines of the GFF3. If anyone knows more about this file format and the conversion process, your help would be greatly appreciated.

head Ppatens_318_v3.3.repeatmasked_assembly_v3.gff3
##gff-version 3
##date 2013-01-03
##sequence-region 516b498fe104e132aeee0db647df660313571851661m500K331
Chr08   RepeatMasker    similarity      500131  500553  22.6    +       .       ID=395262.1;Name=Gypsy-11_PPa-LTR;Target=Gypsy-11_PPa-LTR 24 457
Chr08   RepeatMasker    similarity      500591  501411  23.9    +       .       ID=395262.2;Name=Gypsy-11_PPa-I-int;Target=Gypsy-11_PPa-I-int 1457 2275
Chr08   RepeatMasker    similarity      501414  502856  23.8    +       .       ID=395262.3;Name=Gypsy-11_PPa-I-int;Target=Gypsy-11_PPa-I-int 2554 3997
Chr08   RepeatMasker    similarity      502857  503413   9.2    +       .       ID=395262.4;Name=Gypsy-11_PPa-LTR;Target=Gypsy-11_PPa-LTR 1 557
Chr08   RepeatMasker    similarity      503414  504090  23.6    +       .       ID=395262.5;Name=Gypsy-11_PPa-I-int;Target=Gypsy-11_PPa-I-int 3991 4667
Chr08   RepeatMasker    similarity      504095  504375  24.2    +       .       ID=395262.6;Name=Gypsy-11_PPa-I-int;Target=Gypsy-11_PPa-I-int 4990 5270
Chr08   RepeatMasker    similarity      504376  504825  24.9    +       .       ID=395262.7;Name=Gypsy-11_PPa-LTR;Target=Gypsy-11_PPa-LTR 1 456

Edit: My guess is that in the third column, features are named "similarity" rather than "exon" or "CDS": Does that make sense as a reason? Edit 2: Changing the 3rd column to exon did not make the conversion process work.

cufflinks gff gff3 gtf • 706 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by james.lloyd80
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