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.

	## get all the promoter sequences for human hg19 genome
	## Author: Ming Tang (Tommy)
	## Date: 04/30/2015
	## load the libraries
	library(GenomicRanges)
	library(BSgenome.Hsapiens.UCSC.hg19)
	BSgenome.Hsapiens.UCSC.hg19
	# or
	Hsapiens
	class(Hsapiens)
	##BSgenome contains the DNA sequences
	#############
	library(TxDb.Hsapiens.UCSC.hg19.knownGene)
	Txdb<- TxDb.Hsapiens.UCSC.hg19.knownGene
	Txdb
	class(Txdb)
	## Genomic features, contains the gene structure information
	## all the genes, returns a GRange object
	hg19_genes<- genes(Txdb)
	hg19_genes
	## you can also get all the exons by gene, returns a GRangelist object
	exbg<- exonsBy(Txdb, by="gene")
	exbg
	############### from another database
	library(Homo.sapiens)
	ghs<- genes(Homo.sapiens)
	ghs
	############# hg19_genes and ghs are the same, the ENTREZID is the geneID
	## get all the transcription start sites (TSSs)
	tssgr<- resize( ghs, 1)
	## how many bases you want to extract upstream and downstream of every TSSs
	## in this case, I want the 1500 bases around TSS
	upstream_pad<- 1000
	downstream_pad<- 500
	promoters<- promoters(tssgr, upstream_pad, downstream_pad)
	head(width(promoters))
	## in fact, promoters(ghs, upstream_pad, downstream_pad) gives the same result
	## because the default site for calcuation is the start(ghs), which is the TSS
	### get sequences for all the promoters (1500bp sequences in this case)
	## it takes seconds
	promoter_seq<- getSeq(Hsapiens, promoters)
	## we can annotate the promoter sequences with gene names, symbols in addition to the entrez id.
	annotation<- select(Homo.sapiens, key=names(promoter_seq), keytype="ENTREZID",
	columns=c("SYMBOL", "ENSEMBL", "ENTREZID"))
	dim(annotation)
	## more rows than the promoter_seq
	## Be aware that there are some duplicated rows for the same ENTREZID, because there are multiple ENSEMBL id for the
	## same ENTREZID
	## Let's only use the SYMBOL instead
	annotation<- select(Homo.sapiens, key=names(promoter_seq), keytype="ENTREZID",
	columns=c("SYMBOL", "ENTREZID"))
	## Now, it is the one to one mapping
	## write to a fasta file
	writeXStringSet(promoter_seq, "promoters_1500.fa", append=FALSE,
	compress=FALSE,compression_level=NA, format="fasta")

view raw get_promoter_seq.r hosted with ❤ by GitHub

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