Saccharomyces Genome Database, TSS of protein coding genes

Description

Transcription Start Sites of protein coding genes from the Saccharomyces Genome Database.

Source

Data have been downloaded from Table Browser
Input file format: Tab-delimited TXT

Samples

From Yeast Apr 2011 (NCBI3.1/sacCer3) Assembly

Filename Description Feature GEO-ID
1 sgdGenes.sga TSS from SGD TSS -

Technical Notes

Data was downloaded the 17 August 2015 using the 'Table Browser tool from the UCSC Genome Browser. The resulting TXT file was parsed for genes with a valid protein ID using the following code:

awk '
BEGIN{
  FS=OFS="\t";
  while( (getline < "/db/genome/sacCer3/chr_NC_gi") > 0 ){
    chr["chr" $1] = $2
  }
}
$12 != "n/a" && $1 !~ "bin" {
  if ($4 == "+"){
    start = $5
  }else{
    start = $6
  };
  if (chr[$3] != "") print chr[$3], "TSS", start, $4, 1, $2
}' sacCer3_SDGgenes.txt | sort -k1,1 -k3,3n -k4,4  > sgdGenes.sga

References

  1. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED
    Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. Jan 2012;40(Database issue):D700-5. PMID: 22110037

Genome browser viewable files

None.