Question: Genome repeat masking before gene annotation
gravatar for abhijit.synl
9 days ago by
United States
abhijit.synl30 wrote:

Hello All,

I wanted to know whether repeatmasking a genome or genome fragment, before performing gene annotation, is a good idea. The literature (, and software such as MAKER, and PASA advocate repeatmasking before annotation of genes. Some others say that gene annotation pipelines should be run twice. With and without repeatmasking. I understand the logic behind repeat-masking and then performing gene annotation. However, running a gene annotation on an unmasked genome especially when repeat related genes are not my concern... I don't understand. Therefore looking for answers to the following questions.

1) What are the chances that a non-repeat related gene contains a repetitive region (lets say part of the gag-pol domain is present in a gene, or some exon contains a satellite repeat)? Are there any such cases reported?

2) For genome reference guided transcriptome assembly purposes is it recommended that a masked genome be used? I agree that for expression quantification, this may lead to overestimation or under representation in some cases.

Thank you in advance.

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