ENSEMBL67, ORF starts.

Transcription Start Sites of ENSEMBL database downloaded from Biomart.

• Raw data was downloaded from: BioMart
• Input file format: TXT
• Download date: n/a

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

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	sacCer3_ENSEMBL67.sga	ORF start from ENSEMBL67	TSS	-

The following attributes have been selected:

1. Ensembl Transcript ID
2. Chromosome Name
3. Strand
4. Transcript Start (bp)
5. Transcript End (bp)
6. Gene Start (bp)
7. Gene End (bp)
8. Status (transcript)
9. Status (gene)
10. Associated Gene Name

Then, transcrips have been filtered according to the following rules:

1. Transcript length > 0 [Transcript Start different from Transcript End]
2. Transcript lies on full chromosomes

This can be archived using the following awk command:

awk -F \\t '
$3 == "1" && $4 != $5 {print "chr" $2 "\tTSS\t" $4 "\t+\t" 1 "\t" $10}
$3 == "-1" && $4 != $5 {print $2 "\tTSS\t" $5 "\t-\t" 1 "\t" $10}
' biomart_output.txt | sort -s -k1,1 -k3,3n -k4,4 | compact_sga.pl > ENSEMBL.sga

The SGA file can than be transformed into an FPS file using sga2fps.pl

• Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A
  BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W23-7. doi: 10.1093/nar/gkp265. Epub 2009 May 6. 19420058