Masking repeats in fungal genomes
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3.7 years ago
Morgan S. ▴ 40

Is it necessary to mask repeats in fungal genomes, and if so, is it crucial to do first or can it be done later in the annotation? I have heard arguments that repeat masking may not be necessary, but it seems that it is necessary for annotation pipelines before anything else is done.
Thanks in advance!

annotation fungi repeat masking • 1.1k views
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You can do masking before annotation. Masking can be useful to see repeat elements and their length in genome to get some stats about the genome.

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Great thanks, but is it possible to mask repeats later on in annotation pipeline?

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You mean masking during annotation? Why do you do this? In annotation, you will try to find function of genes, so you already have gene sequences. But in genome there are genes and other non-coding sequences in which you need to find repeats. To me, you can mask genome. Because in annotation you know genes but you try to find their functions etc. If your annotation pipeline includes or starts from genome data, you can include masking in your pipeline, but keep in your mind you need to mask genome not genes.

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