ENSEMBL, TSS collection downloaded from ENSEMBL.

TSS collection provided by ENSEMBL.

• Raw data was downloaded from: Biomart
• Input file format: TXT
• Download date: 29-11-2016

From D. melanogaster (Apr 2006 BDGP R5/dm3).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	Dm_ENSEMBL70.sga	TSS from ENSEMBL70	TSS	-
2	Dm_ENSEMBL66.sga	TSS from ENSEMBL66	TSS	-
3	Dm_ENSEMBL64.sga	TSS from ENSEMBL64	TSS	-
4	Dm_ENSEMBL86.sga	TSS from ENSEMBL86	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
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

• 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