[maker-devel] FW: maker-control file

[Carson Holt]

On 3/5/14, 11:59 AM, "Borhan, Hossein" <Hossein.Borhan at AGR.GC.CA> wrote:

>Dear Maker users
>
>I want to run maker on a fungal genome of about 45 Mb with about 1/3 of
>the genome begin repeat rich. But most of the virulent genes are located
>within the repeat regions flanked but stretch of repeats. I am not sure
>if I  use the repeat masker option I am going to miss out on the
>predication of these virulent genes located within the repeats.
>
>Other concerns with the setting in maker-opts file for fungal genomes are:
>
>single_exon = 0     should this get changed to 1 since single exon genes
>are quit common in fungi and what is the consequence of this on using EST
>and assembled RNA as evidence for gene prediction
>
>correct_est_fusion=0                  #limits use of ESTs in annotation
>to avoid fusion genes         as I understand this option will remove the
>overlapping UTRs but what is the consequence of setting this option on
>the use of EST for predicting ORFs
>
>
>Thanks
>
>
>
>HB
>
>
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>