[maker-devel] FW: maker-control file

[Carson Holt]

Not using repeat masking will cause many problems.  Beside a gene being
flanked by repeats does not mean it will be lost, any evidence/alignments
that can seed in non-repetative regions (gene/exon) are still allowed to
extend into repetitive regions during the polishing stage (aligners have
two stages - seed and extend).  So transposons should never seed, but
genes will because there sequence will contain non-repetative regions
(even if they are near repeats).

single_exon should be set to 1 for fungi, just make sure to set the
minimum length of single exon evidence to something reasonable like 250bp.

correct_est_fusion should not be used together with est2genome.  It won’t
fail, you just get odd results.  Actually est2genome should not ever be
used to generate the final annotation set.  It is a convenience method
that allows you to generate rough models for training gene predictors like
SNAP and Augustus.  But once they are trained it should be turned off,
because the models it produces will be partial (Ests rarely cover the
whole transcript) and the results will have many false potties from
background transcription events from your EST data.  These models are good
enough to train with, but make very poor final annotations. So in the end
you should be using correct_est_fusion=1 with the SNAP pr Augustus set and
not est2genome (which should already have been turned off by then).


Thanks,
Carson


>
>
>On 3/5/14, 11:59 AM, "Borhan, Hossein" <> 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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