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  • joseph
    Member
    • Feb 2008
    • 39

    bed file around the TSSs

    Hi
    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:
    Code:
    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	-
    Thanks
    Joseph
  • malachig
    Senior Member
    • Aug 2010
    • 117

    #2
    Have you considered using the EnsEMBL API for these kinds of tasks?

    Ensembl API docs

    Comment

    • adamdeluca
      Member
      • Jul 2010
      • 95

      #3
      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:
      Code:
      awk '{print $1"\t"$2-349"\t"$2+350}' file > TSS.bed

      Comment

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