integrate gmap into Maker

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integrate gmap into Maker

Wen Yao

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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Re: integrate gmap into Maker

Daniel Ence-2
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 <[hidden email]> 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

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org