[maker-devel] About loss of Histone H2A, H2B, H4

[Quanwei Zhang]

Dear Carson:

Thank you for your comments and suggestions. Now the SNAP was trained with
repeat masked, is it necessary to retrain the predictor without repeat
masking?
By BUSCO analysis on the genome, the completeness is shown as below. Now I
am doing the analysis using the default reports of Maker2 (i.e., gene
models with evidence support, the default build). For the gene loss,
besides you suggestions I am also considering to do the analysis using the
gene models with evidence support plus those with scanned domains (i.e.,
standard build). How do you think?


C:95.0%[S:92.7%,D:2.3%],F:2.2%,M:2.8%,n:4104

  3902  Complete BUSCOs (C)

  3806  Complete and single-copy BUSCOs (S)

  96  Complete and duplicated BUSCOs (D)

  92  Fragmented BUSCOs (F)
  110  Missing BUSCOs (M)

Thanks
Best
Quanwei


2017-11-21 11:19 GMT-05:00 Carson Holt <carsonhh at gmail.com>:

> No known biases, but if you are concerned, you can collect known Histone
> H2A, H2B, H4 proteins and transcripts from other species (protein= and
> altest= options), them run MAKER with no masking to see if you gain any
> models that may have been overlooked because of over-masking of repeats.
> Make sure to evaluate any models you find as being a pseudogene. Run
> InterProScan on results to make sure they contain known InterPro domains
> for that gene family as well. Running without repeat masking will increase
> sensitivity but also false positives derived from low homology alignments
> to simple repeats which is why you need to evaluate results using something
> like InterProScan.
>
> Also run BUSCO to evaluate the completeness of the genome. Make sure that
> the observed contraction is not just a result of an incomplete assembly.
>
> —Carson
>
>
> On Nov 16, 2017, at 12:46 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>
> Hello:
>
> We have annotated a new rodent genome using Maker2. Based on the annotated
> maker2 gene sets, we did gene family expansion/contraction analysis using
> CAFE. We found Histone H2A, H2B, H4 gene families are under contraction. I
> wonder whether there are known bias to predict those gene families using
> Maker2? For example, can this due to repeat masking of the genome? I used
> repeatmaker and generated species specific repeat libraries follows
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/
> Repeat_Library_Construction--Basic.
>
> Thanks
>
> Best
> Quanwei
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>
>
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