[maker-devel] integrate gmap into Maker

[Daniel Ence]

Without commenting on the merits of GMAP vs Blastn or Exonerate, you can provide evidence alignments from any source in gff format in the maker control files. I think for GMAP this would mean converting the sam/bam outputs to a gff3 format, but I don’t know those steps of the top of my head. 

~Daniel 




> On Sep 24, 2017, at 5:08 AM, Wen Yao <venyao at qq.com> wrote:
> 
> Dear Guys,
> 
>  
> 
> I am using Maker to annotate my genome sequence. However, it costs too much time.
> 
> By default, Maker use Blastn and Exonerate to align EST or assembled transcripts to the genome.
> 
> I am wondering if I can use GMAP to align the assembled transcripts to the genome and then provide the
> 
> alignment to Maker. If so, this may save much time, as GMAP is very fast.
> 
> 
> 
> Thanks!
> 
>  
> 
> Best regards,
> 
>  
> 
> Wen Yao
> 
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