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

[Quanwei Zhang]

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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