[maker-devel] Non-redundant Reference Human EST Data

[Carson Holt]

Hi Julian, 

Using Human EST’s on primate contigs would be very inefficient. The human genome is already annotated, so you should instead use either the human proteome or human transcripts as input.  Using EST’s from another species other than the one being annotated should only be done if there is not a curated annotation set to use instead. 

You may be able to just give the human transcripts to the est= option if the two organisms have not diverged too much in nucleotide sequence.  Don’t use the alt_est option since you have human protein annotations.  The alt_est option uses tblastx to seed the alignments which will not be as accurate as the protein= option that seeds via blastx, and it is about 10 time more expensive computationally. So it will take a lot longer and you won’t get anything that you couldn’t have found using the protein data instead.

Also scaffolds shorter than about 10kb will likely be too short to annotate, so you can test out your parameters on a few of only the largest contigs. In addition, don’t use SNAP because it performs poorly on primate genomes (use Augustus instead).

Thanks,
Carson



> On May 14, 2015, at 12:17 PM, Julian Egger <julian.egger at omahazoo.com> wrote:
> 
> We have assembled scaffolds from genomic reads of a primate sample and would like to annotate as many genes as possible with MAKER.  Where is the best place to find an EST file to use with MAKER containing all of the non-redundant reference humans ESTs?  Was trying to look around NCBI, Ensembl, and UCSC, but not sure what the ftp site, subdirectory, and file name would be for something like that.
> 
> Thanks  
> 
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