ENSEMBL61, 5\'end collection.

Interspliced Sites of ENSEMBL61 database downloaded from Biomart.

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

From C. elegans (May 2008 WS190/ce6).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	Cen_ENSEMBL61.sga	5p-end from ENSEMBL61	5END	-

Data was downloaded from BioMart selecting the following attributes:

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
3. Gene must have a 5' UTR [Transcript Start different from Gene Start]
4. Genes must be annotated [Associated Gene Name present]
5. Gene and transcripts status known

This can be archived using the following awk command:

awk -F \\t '
$2 ~ "^[0-9][0-9]?|^[XY]" && $3 == "1" && $4 != $5 && $4 != $6 && $10 != "" && $8 == "KNOW" && $9 == "KNOW" {print "chr" $2 "\tTSS\t" $4 "\t+\t" 1 "\t" $10}
$2 ~ "^[0-9][0-9]?|^[XY]" && $3 == "-1" && $4 != $5 && $5 != $7 && $10 != "" && $8 == "KNOW" && $9 == "KNOW" {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