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Thursday, April 30, 2015

get all the promoter sequences of human hg19 genome

One of my former friends (a biologist who does not know much about computer) wants me to help her to get all the promoter sequences from the human genome. It is a very simple task and I think all the biologists should know how to do it. There are many ways to do it, but I will show you how to do it using bioconductor.

Using less I see all the sequences are there, to make sure the sequences are right, one can manually inspect the UCSC genome browser for several sequences.

I really do not want to dig in (google is your friend) to find a way to write the name using the SYMBOL rather than the ENTREZID....
You can convert the gene ids by many ways too.
I have two posts for that http://crazyhottommy.blogspot.com/2014/09/converting-gene-ids-using-bioconductor.html
and http://crazyhottommy.blogspot.com/2014/09/mapping-gene-ids-with-mygene.html
In addition, I prefer to prepare a bed file for all the promoters using bedtools slop (RefSeq table from UCSC, or from a GENCODE GTF file). Then, use bedtools to extract DNA sequences using bedtools getfasta. To me, it is more flexible on the command lines.
see my previous post here http://crazyhottommy.blogspot.com/2015/02/fetch-genomic-sequences-from-coordinates.html

3 comments:

  1. it's very useful to combine the R package BSgenome.Hsapiens.UCSC.hg19 and TxDb.Hsapiens.UCSC.hg19.knownGene . In fact, most of the bioconductor packages are designed to replace the small script in Linux.
    And I believe you are a Chinese , yes or right ?
    If yes, maybe we can talk more with each other

    ReplyDelete
    Replies
    1. YES, I am a Chinese. Nice to meet you.

      Delete
  2. hi, very usefull, im trying to do the same thing but using maize (Zea mays)

    I want to get promoters and analyse some regulatory elements and plot them

    how do i do?

    greatings

    ReplyDelete