Saccharomyces Genome Database, TSS of protein coding genesp.

Description

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

Source

Samples

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

Genome Annotation:

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

Technical Notes

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
	

References

Last update: 11 Oct 2017