Gaps Size
2
0
Entering edit mode
12.4 years ago

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

alignment • 1.8k views
ADD COMMENT
2
Entering edit mode

even one base...

ADD REPLY
0
Entering edit mode
12.4 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.

ADD COMMENT
0
Entering edit mode

why would it have to be ngs related?

ADD REPLY
0
Entering edit mode
12.4 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.

ADD COMMENT

Login before adding your answer.

Traffic: 1789 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6