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  • TSS for encode data

    HI,

    i am new to chip-seq data analysis and right now i need to develop heatmaps to compare my data with the histone encode data (H3K4me3 and K27me3)

    where do i get the TSS annotation files to compare?

    Is there any good tool or software that compares the data between them

    Thanks

  • #2
    I'm not sure what are you asking exactly, but

    you can get RefSeq annotation from USCS genome browser:



    then you can use PeakAnnotator to see how your chip-seq data aligns with respect to RefSeq TSS

    Comment


    • #3
      i need to develop a heatmap to compare my chipseq data with the encode tss data

      for example like the image on the top of this page



      i want to compare my data with H3K4ME3 and H3K27me3

      for TSS this should i follow this steps

      Go to the Tables section of UCSC (http://genome.ucsc.edu/cgi-bin/hgTables)
      Set each field to the following values:
      Clade: Mammal
      Genome: human
      Assembly: hg19
      Group: Genes and Gene Prediction Tracks
      Track: RefSeq Genes
      Table: refGene
      Output format: BED - Bed Extensible Data
      Click on Get output
      On the next screen select Upstream by and set its value to 1
      Click on Get BED

      thank you

      Comment

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