Entering edit mode
7.0 years ago
AA Kamran
•
0
I tried to extract the bidirectional promoters using the syntax below-
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19
mysql> select K1.chrom,K1.name,K2.name,K1.strand,K2.strand,
LEAST(K1.txStart,K1.txEnd,K2.txStart,K2.txEnd) as L,
GREATEST(K1.txStart,K1.txEnd,K2.txStart,K2.txEnd) as R
from
knownGene as K1,
knownGene as K2
where K1.chrom=K2.chrom and
( (K1.strand='+' and K2.strand='-' and ABS(K1.txStart-K2.txEnd) < 1000) or
(K1.strand='-' and K2.strand='+' and ABS(K1.txEnd-K2.txStart) <1000) )
;
Unfortunately after using this syntax this shows me this error-
" BIGINT UNSIGNED value is out of range"
I tried to use this before my syntax-
SET sql_mode = 'NO_UNSIGNED_SUBTRACTION';
This solved the error but after a certain period of time the query gets terminated showing-
"lost connection during query"
I don't know if i should try this-
"max_allowed_packet=32M"
Apart from this i think i have used the syntax which was used 5 years ago but what should be the syntax for the current version of the UCSC mysql????
TIA.