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Question: GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
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gravatar for JunLVI
7 days ago by
JunLVI30
Japan
JunLVI30 wrote:

 

Hi, I was trying to trying counts reads mapped onto a bed file, 

I checked the workflow of "DESeq2" , 

    gtffile <- ("mm9genes.gtf") 
    library("GenomicFeatures")
    (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character()))
    (ebg <- exonsBy(txdb, by="gene"))
    library("GenomicAlignments")
    library("BiocParallel")
    register(MulticoreParam())
    se <- summarizeOverlaps(features=ebg, reads=bamfiles,
                             mode="Union",
                            singleEnd=TRUE,
                           ignore.strand=TRUE,
                          fragments=FALSE )  

I am not sure I understood the code completely, but my understanding is that they extract the exons locations grouped by genes (by using GenomicFeatures packages), and do the counting. 

but what if I want to count the reads overlap with genomic features described in a bed file or gtf converted from the bed file? the counterpart of "ebg" in the example.

 

 

 

 

ADD COMMENTlink modified 6 days ago by James W. MacDonald42k • written 7 days ago by JunLVI30
0
gravatar for James W. MacDonald
6 days ago by
United States
James W. MacDonald42k wrote:

I think you misunderstand the code. You are defining genomic regions of interest (exons), based on the GFF file, and then you are counting up all the reads from your bamfiles that overlap these regions of interest, using summarizeOverlaps.

ADD COMMENTlink written 6 days ago by James W. MacDonald42k
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