[mira_talk] Re: gff to gff3
- From: Andrej Benjak <abenjak@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 23 Oct 2014 12:38:21 +0200
This thread has turned into 2 topics:
1) is it necessary to convert gbk to a gff in order to use it in MIRA as
ref:
NO, the gbk is totally fine as reference format.
Gbk and gff (and some others) contain the same information, just in
different formats.
2) can I use miraconvert to produce a gff3 file?
Yes, in principle, but we just found out that there seems to be a bug in
converting gbk to gff3 with miraconvert.
If you desperately need a gff file, a simple way is to load the gbk into
Artemis (http://www.sanger.ac.uk/resources/software/artemis/) and export
it as gff.
Cheers,
Andrej
On 10/23/2014 11:31 AM, Felipe Lira wrote:
Thank you Bastien,
In this case would be appropriate convert a .gbk file to .gff3 using
miraconvert or you don recommend it?
Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
/Microbial Biotechnology Department/
Fellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario
hacerlo.
/Before you print this e-mail, think well if it is //really// necessary./
El Jueves 23 de octubre de 2014 11:06, Bastien Chevreux
<bach@xxxxxxxxxxxx> escribió:
On October 23, 2014 at 10:25 AM Andrej Benjak <abenjak@xxxxxxxxx> wrote:
To use a gff file as reference in MIRA make sure the nucleotide
sequence is embedded in the file, then it should work.
(most gff files out there, including those from NCBI, don't contain
any sequence)
Albeit if the GFF3 does not have the sequence embedded, you can load
it from a separate file (like the data you get from the NCBI). E.g.:
readgroup
...
data= somefile.fnadata = somefile.gff3
You just need to take care that the sequence file really is the one
belonging to the GFF3 file. MIRA can catch a number of mix-up cases,
but not all. Therefore, GFF3 with sequence embedded is my recommended
approach.
B.
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