Gaps Size
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10.6 years ago

What's the size of a gap in an alignment to be considered a deletion?

alignment • 1.5k views
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even one base...

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10.6 years ago

One base: e.g: http://www.ncbi.nlm.nih.gov/pubmed/9621520 (not a ngs-related paper, but it shows that any deletion matters)

J Hum Genet. 1998;43(2):135-7. A one-base deletion (183delC) and a missense mutation (D276H) in the T-protein gene from a Japanese family with nonketotic hyperglycinemia.

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why would it have to be ngs related?

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10.6 years ago
Geparada ★ 1.5k

If you are aligning DNA-seq against a genome, all the gaps are candidates to be a deletion. But if you are aligning eukaryotic RNA-seq against a genome, gaps longer than 40 pb that have canonical boundaries (GT-AG, GC-AG or AT-AC) are introns. The smaller gaps are more likely to be a deletion than a intron, because the splicing machinery it's a very large RNA-protein complex that needs to fit on the splice junction sequences in order to process the intron.

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