Extracting Bidirectional promoters from UCSC mysql server gives error....
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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.

software error sequence Assembly UCSC mysql • 1.1k views
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