Stream: genomics
Topic: readCoverage
Gaston Fiore (May 20 2016 at 19:20):
@ Bob Milius and whoever else reads this, I cannot find a definition for readCoverage in the SO. What do you suggest that I do? Thanks!
Bret H (May 31 2016 at 15:21):
'read Coverage' is a technical term indicating how many reads 'cover' (overlap) on a particular nucleotide. I would suggest defining it as a composite of 'reads' (SO:0000150) that overlap at a specific nucleotide. I think this should be a SO:0001686 (quality value) of a nucleotide within a sequence.
Joel Schneider (May 31 2016 at 21:57):
The GVF specification appears to be the only documentation on the SO site that mentions coverage. The specification defines pragmas for encoding average coverage as an attribute of the technology platform: http://www.sequenceontology.org/resources/gvf.html
Joel Schneider (May 31 2016 at 22:29):
The sequence ontology shows a detailed hierarchy leading from read (SO:0000150) to sequence_feature (SO:0000110): SO:0000150_lg.png
However, the ontology does not specifically mention coverage. Nailing down a generic definition for read coverage and/or quality value may be difficult, because the method for computing it may vary depending on details of the sequence data and assembly method (or technology platform).
Last updated: Apr 12 2022 at 19:14 UTC
