I am working on a NGS database using MySQL and I found a problem to create the table for coverage data. Each row contains an interval of the entire exome sequenced.
The problem I found is related to the exons because in most cases there is more than one exon and they are separated by commas, for example: "1, 2, 3". As the exons are numbers, creating an extra table is a nonsense and using ENUM is not an option as there is no maximum number. I think the best solution is consider the field as text but, is it correct?
Here you have an example: https://www.db-fiddle.com/f/38SWtKrqWpqZJRVZbw28SC/21
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Swimming bird •
normalize, normalize, normalize
https://en.wikipedia.org/wiki/Database_normalization
create a table for each chromosome, transcript, exon
Do you mean 3 tables or only one that includes chromosome, transcripts and exons?
something like
create table chromosome (id int,name varchar,length int);
create table transcript (id int,chromosome_id int, name varchar);
create table exon (id int,transcript_id int, chromStart int,chromEnd int);
create table coverage(int exon_id int,coverage int);
In case there are 3 exons I suppose there will be 3 different records in the coverage table, right?
Do you know any example of a database that store coverage data? I couldn't find any.
In case there are 3 exons I suppose there will be 3 different records in the coverage table, right?
yes
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Hello Swimming bird!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/8867
This is typically not recommended as it runs the risk of annoying people in both communities.
Ok, sorry. I deleted the post on stackexchange.