Extract Refseq Genes From Ucsc

Question

[Radhouane Aniba]

Hello everyone

I am trying to get all human RefSeq genes from UCSC using MySQL query such as :

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select * from knownGene'

What kind of modification I have to do to extract only unique RefSeq genes and not all related transcripts to each record.(CDS ? which table ?)

Kindly

Rad

Answer 1

[Pierre Lindenbaum]

use refGene instead of knownGene.

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select * from refGene limit 2\G'
*************************** 1. row ***************************
         bin: 585
        name: NR_028269
       chrom: chr1
      strand: -
     txStart: 4224
       txEnd: 7502
    cdsStart: 7502
      cdsEnd: 7502
   exonCount: 7
  exonStarts: 4224,4832,5658,6469,6719,7095,7468,
    exonEnds: 4692,4901,5810,6631,6918,7231,7502,
       score: 0
       name2: LOC100288778
cdsStartStat: unk
  cdsEndStat: unk
  exonFrames: -1,-1,-1,-1,-1,-1,-1,
*************************** 2. row ***************************
         bin: 585
        name: NR_026818
       chrom: chr1
      strand: -
     txStart: 24473
       txEnd: 25944
    cdsStart: 25944
      cdsEnd: 25944
   exonCount: 3
  exonStarts: 24473,25139,25583,
    exonEnds: 25037,25344,25944,
       score: 0
       name2: FAM138A
cdsStartStat: unk
  cdsEndStat: unk
  exonFrames: -1,-1,-1,

[Radhouane Aniba]

Thanks Pierre for the tip

[Radhouane Aniba]

it is strange that cdsStart and cdsEnd have same content, isn't it ?

[Pierre Lindenbaum]

these are non-coding genes.