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Old 10-13-2010, 09:01 AM   #1
Location: ca

Join Date: Feb 2008
Posts: 39
Default bed file around the TSSs

I would highly appreciate if you could show me how to create a bed file around the TSSs from UCSC databases such as ensembl or refSeq genes. I need 350 nucleotides upstream and 150 nucleotides downstream of TSSs. The bed file should look like below, where:
chromStart is 350 nucleotides upstream of TSS
chromEnd is 150 nucleotides downstream of TSS
name is Name of gene or transcript_id depending on the database.

chrom	chromStart	chromEnd	name		score	strand
chr1	67051159	67163158	NM_024763	0	-	
chr1	67075869	67163158	NM_207014	0	+	
chr1	16762998	16812569	NM_017940	0	-
joseph is offline   Reply With Quote
Old 10-13-2010, 10:10 AM   #2
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Location: WashU

Join Date: Aug 2010
Posts: 117

Have you considered using the EnsEMBL API for these kinds of tasks?

Ensembl API docs
malachig is offline   Reply With Quote
Old 10-13-2010, 11:32 AM   #3
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95

On the UCSC table browser go to the "Genes and Gene Predictions" group, select the table you want (ensGene, refGene, etc). Change the output format to "Selected fields..." and on the next page select the chr and the TSS. You can then pad the TSS by doing something like:
awk '{print $1"\t"$2-349"\t"$2+350}' file > TSS.bed
adamdeluca is offline   Reply With Quote

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