Question: genes upstream or downstream of a LNcRNA
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gravatar for Explorer
11 months ago by
Explorer70
Australia
Explorer70 wrote:

Hi

I have the list of LncRNAs of interest and their coordinates in BED format. I am interested in identifying the protein coding genes that are 300kb upstream and 300kb downstream of each of those LncRNAs. The genome annotation of lncRNA is gencode 27. I would like to how I can find the upstream/downstream genes? The easiest way I can think is table browser in UCSC browser.

But I am not sure how. Please help with this.

Thanks for your time.

rna-seq • 446 views
ADD COMMENTlink written 11 months ago by Explorer70

Not solution but a direction. You will require coordinates of protein coding genes in BED format.

step#1 : fetch the coordinates 300 kb up and downstream of the LncRNAs. You may use awk or shell or a simple PERL one liner for that. Pipe that into a standard BED file format.

step#2 : use bedtools intesect to find the overlapping regions using the BED file for protein coding genes.

That's how I think! there should be other faster and better ways.

ADD REPLYlink written 11 months ago by lakhujanivijay4.5k

Go through this post. It might help.

ADD REPLYlink written 11 months ago by toralmanvar820
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