Saccharomyces Genome Database, TSS of protein coding genesp.

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

• Raw data was downloaded from: UCSC Table Browser
• Input file format: TXT
• Download date: 17-08-2015

From S. cerevisiae (Apr 2011 R64/sacCer3).

Genome Annotation:

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

Data was downloaded 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
	

• 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. 2012 Jan;40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. Epub 2011 Nov 21. 22110037