User:Lindenb/Notebook/UMR915/20100629

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20100628        Top        20100630       


creating table for degenerate base

will help to map degenerate prediction (sift/pph2) to the pileup calling.

 create table deg2base(symbol char(1) not null, base enum ('A','T','G','C') not null, index(symbol), constraint unique index(symbol,base));
 insert into deg2base(symbol,base) values ('A','A'),('C','C'),('G','G'),('T','T');
 insert into deg2base(symbol,base) values ('N','A'),('N','C'),('N','G'),('N','T');
 (...)


symbol	base
A	A
B	T
B	G
B	C
C	C
D	A
D	T
D	G
G	G
H	A
H	T
H	C
K	T
K	G
M	A
M	C
N	A
N	T
N	G
N	C
R	A
R	G
S	G
S	C
T	T
V	A
V	G
V	C
W	A
W	T
Y	T
Y	C

Format FAIDX

example:

chr9_random	1146434	2938571700	50	51
chrM	16571	2939741069	50	51
chrX	154913754	2939757978	50	51
chrX_random	1719168	3097770021	50	51
chrY	57772954	3099523579	50	51
  • column 1: sequence name
  • column 2: sequence length
  • column 3: file offset for the first base in the file
  • column 4: fasta one line size
  • column 5: column 4 +1  ?? (CRLF would be 52 ??)
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