[maker-devel] MAKER and RepeatModeler

[Shaun Jackman]

Hi, Carson.

I removed two small contaminant contigs (~7 kbp) from the assembly (~6 Mbp), and MAKER found four fewer genes, four copies of the same atp8 gene, but these genes were not in the contaminant contigs.

I figured out that it’s because I’m running RepeatModeler to create the rmlib for MAKER. When I remove the contaminant contigs, RepeatModeler now identifies this gene atp8 as being a LTR/Gypsy repeat.

Any thoughts on why removing two contigs would cause RepeatModeler to identify new repeats?

Cheers,
Shaun



-- 
http://sjackman.ca/
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