[maker-devel] mRNA-seq data

[Carson Holt]

Yes.  If you have them in fasta format, just provide them to the est= option
and let MAEKR align them with exonerate.  If you used something like
cufflinks or trinity, to process them you can provide them to the est_gff
option (MAKER comes with a cufflinks2gff3 converter to make that easy).

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Wed, 4 Apr 2012 02:24:49 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mRNA-seq data

Hi,

 

I am using to MAKER to annotate a genome and I would like a couple of
clarifications.

 

In the previous version of MAKER, under EST_evidence in maker_opts. ctl the
user could input est and est_reads- the mRNAseq reads (although this was not
fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation
quality.

I have assembled transcriptome data from Sanger,454 and Illumina

 

Do I just provide all this data in a fasta file format to the 'est' option?
Is this is the best way to provide the mRNA-seq evidence?Will this assure
the mRNA-seq data is used to improve the annotations?

 

Thanks!

 

Ranjani
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