Looking process to convert gff3 format into ace format or sam format

andylai · 05-16-2011, 08:47 PM

Is there any application can convert gff3 file and related fasta files into ace file or sam file? I dont want to reinvent the wheel.

maubp · 05-17-2011, 03:09 AM

I don't understand what you want to do - going from GFF3 to ACE or SAM makes no sense.

You store annotation in GFF3 files (e.g. there is a gene at this location), but neither ACE nor SAM hold that kind of annotation (they are assembly/mapping files, e.g. this read mapped to this contig at this location).

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05-16-2011, 08:47 PM	#1
andylai Junior Member Location: Australia Join Date: Apr 2010 Posts: 6	Looking process to convert gff3 format into ace format or sam format Is there any application can convert gff3 file and related fasta files into ace file or sam file? I dont want to reinvent the wheel.

05-17-2011, 03:09 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	I don't understand what you want to do - going from GFF3 to ACE or SAM makes no sense. You store annotation in GFF3 files (e.g. there is a gene at this location), but neither ACE nor SAM hold that kind of annotation (they are assembly/mapping files, e.g. this read mapped to this contig at this location).