Question: ATAC-seq : strategies to have the list of the expressed genes
0
gravatar for anais1396
4 months ago by
anais139620
Brussels
anais139620 wrote:

Hello everyone !!

I'm new in the analyse of NGS data and I have ATAC-seq datas. I would like to know what is the strategies used to obtain a list with the expressed genes from the .bed files that we have after the peak calling ?

I performed peak calling with macs2 and I obtained bed files (narrowPeak) which contain the list of positions in genome where the chromatin is open. I would like to know how to obtain (from these bed files) the list of the genes which are in these regions because these should be the genes that will be expressed in my cells as the chromatin is open so we can have potentially TF binding in these regions. Then, I have to compare 2 conditions (healthy people and patient) so I have to compare 2 lists of genes that I will obtain. Is there a tool to do that ?

Thank you in advance for your help !!

Anaïs

sequencing atac-seq • 470 views
ADD COMMENTlink modified 3 months ago • written 4 months ago by anais139620

Can you tell us which genome assembly you aligned your NGS data to?

ADD REPLYlink written 4 months ago by James Ashmore2.5k

I used the human genome, hg19 version

ADD REPLYlink written 4 months ago by anais139620

I tried to load required packages but it doesn't work...

I have the following error message :"installation path not writeable, unable to update packages: MASS, survival" for the loading of bioclite() and then I have this "installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status"

I would try to do this with R but I'm not very familiar with it...

Little help please ???

Thanks in advance ;-)

ADD REPLYlink written 3 months ago by anais139620
1

Follow these directions to set a local storage path (adjust file paths as needed for your local environment) for your R packages.

Note: Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax56k
2
gravatar for James Ashmore
4 months ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

If you have R and Bioconductor installed, you can try the following steps:

# Load required packages
pkgNames <- c("rtracklayer", "org.Hs.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene")
libSetup <- lapply(pkgNames, library, character.only = TRUE)

# Import narrowPeak file
fileName <- "Replace this string with the name of your peak file"
narrowPeak <- c(signalValue = "numeric", pValue = "numeric", qValue = "numeric", peak = "integer")
peakRanges <- import(fileName, format = "BED", extraCols = narrowPeak)

# Extract promoter ranges
promRanges <- promoters(genes(TxDb.Hsapiens.UCSC.hg19.knownGene))

# Map gene symbol names
promRanges$symbol <- mapIds(org.Hs.eg.db, promRanges$gene_id, "SYMBOL", "ENTREZID")

# Find overlapping ranges
rangeOverlaps <- findOverlaps(peakRanges, promRanges)
peakRanges$symbol <- promRanges$symbol[subjectHits(rangeOverlaps)]

The peakRanges object will then have a column with the gene names of the promoters your peaks overlap. If you are not familiar with R or don't have them installed, you can go to the UCSC Table Browser and download a BED file of the promoter regions. Then use a tool such as Bedtools or Bedops to intersect your narrowPeak file with the BED file:

bedtools intersect -a Peaks.narrowPeak -b Promoters.bed
ADD COMMENTlink modified 4 months ago • written 4 months ago by James Ashmore2.5k

Thank you very much for your answer, it is very helpful !!

Where do you have the files with the promoters in R? I will also need them with the hg38 version of the human genome Or maybe just in switching the hg19 into hg38 in the name of the file in R ??

ADD REPLYlink modified 4 months ago • written 4 months ago by anais139620
1

There is a hg38 package for TxDb (http://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg38.knownGene.html ). Data for promoters is coming from this package.

ADD REPLYlink written 4 months ago by genomax56k

Thank you !! It's very helpful !!

ADD REPLYlink written 3 months ago by anais139620
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